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Salam MTB, Kataoka R. Changes in the Endophytic Bacterial Community of Brassica rapa after Application of Systemic Insecticides. Int J Mol Sci 2023; 24:15306. [PMID: 37894986 PMCID: PMC10607537 DOI: 10.3390/ijms242015306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Insecticides not only control target pests but also adversely affect non-target communities including humans, animals, and microbial communities in host plants and soils. The effect of insecticides on non-target communities, especially endophytic bacterial communities, remains poorly understood. Two phases of treatments were conducted to compare the trends in endophytic bacterial response after insecticide application. Endophytic bacteria were isolated at 2 and 4 weeks after germination. Most insecticide treatments showed a declining trend in bacterial diversity and abundance, whereas an increasing trend was observed in the control. Therefore, insecticide use negatively affected non-target endophytic bacterial communities. Bacillus spp. was mostly dominant in the early stage in both insecticide treatment and control groups. Nevertheless, in the matured stage, mostly bacteria including Pseudomonas spp., Priestia spp. were dominant in groups treated with high insecticide concentrations. Therefore, plants can regulate and moderate their microbiome during their lifecycle depending on surrounding environmental conditions.
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Affiliation(s)
- Md. Tareq Bin Salam
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
- Soil, Water and Environment Discipline, Khulna University, Khulna 9208, Bangladesh
| | - Ryota Kataoka
- Faculty of Life and Environmental Sciences, University of Yamanashi, Kofu 400-8510, Yamanashi, Japan;
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Allen WJ, Waller LP, Barratt BIP, Dickie IA. Puke or poop? Comparison of regurgitate and faecal samples to infer alpine grasshopper ( Paprides nitidus Hutton) diet in experimental plant communities. Ecol Evol 2023; 13:e10444. [PMID: 37649704 PMCID: PMC10463123 DOI: 10.1002/ece3.10444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023] Open
Abstract
Characterising plant-herbivore interactions is important to understanding the processes that influence community structure and ecosystem functioning. Traditional methods used to identify plant-herbivore interactions are being superseded by non-destructive molecular approaches that can infer interactions with greater resolution and accuracy from environmental DNA (e.g. faeces and regurgitate). However, few studies have compared the success of using different sample types and whether they provide similar or contrasting information about species' diet. Here we compared the success of DNA amplification and host plant species identification using restriction fragment length polymorphism (RFLP) applied to faecal and regurgitate samples collected from alpine grasshoppers Paprides nitidus Hutton during a grassland community mesocosm experiment. We found that DNA amplification success was 23% and 86% higher for faecal than regurgitate samples from female and male grasshoppers, respectively. In contrast, successful host plant identification using RFLP was 9% higher for regurgitate than faecal samples. The mean number of host plant species identified per sample (1.40) did not differ between sample types or grasshopper sexes. Of the 136 paired faecal-regurgitate samples, just 41% and 74% produced exactly or partially matching host plant identifications, respectively, indicating that different sample types provided complementary information about herbivore diet. Some plant species were more likely to be identified from faecal samples than expected by chance, and we found that this identification bias skewed towards plant species with higher investment in leaf tissue. We conclude that multiple sample types may be required to fully characterise an invertebrate herbivore species' diet.
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Affiliation(s)
- Warwick J. Allen
- Bio‐Protection Research Centre, School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
- Present address:
Manaaki Whenua ‐ Landcare Research76 Gerald StreetLincoln7608New Zealand
| | | | - Barbara I. P. Barratt
- AgResearch, Invermay Research CentreMosgielNew Zealand
- Department of BotanyUniversity of OtagoDunedinNew Zealand
| | - Ian A. Dickie
- Bio‐Protection Research Centre, School of Biological SciencesUniversity of CanterburyChristchurchNew Zealand
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Nigam N, Sinha S, Verma N, Gupta H, Fatima G, Gupta S, Kumar P. To Study the β-Globin Haplotype Pattern of Descent of a Set of Linked Alleles Occurring on the Same Chromosome in the Northern Province of India. Cureus 2023; 15:e36569. [PMID: 37095793 PMCID: PMC10122190 DOI: 10.7759/cureus.36569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2023] [Indexed: 04/26/2023] Open
Abstract
OBJECTIVE To study the five mutations commonly prevalent in North India, i.e., IVS-I-5 (G→C), 619 bp deletion, IVS-I-1 (G→T), codon 41/42 (-TTCT), and codon 8/9 (+G), in the beta thalassemia (β-thalassemia) major children. The specific β-thalassemia mutations of different haplotype patterns of the β-globin gene cluster will also be determined. METHODS A total of 125 children diagnosed with β-thalassemia major visiting the Department of Pediatrics of King George's Medical University were involved in the study. As per the QIAamp (Qiagen, Hilden, Germany) manufacturer guidelines, genomic DNA was isolated from whole blood. To identify the haplotype pattern within the β-globin gene cluster, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was used. The respective restriction endonucleases used were Hind III/GƔ, Hinc II/Ψß, Hinf I/ß, Ava II/ß, and BamHI for the haplotype analysis in the β-globin pattern of descent of a set of linked alleles occurring on the same chromosome. RESULTS Among the five common mutations, 73 patients had IVS-I-5 (G→C), 28 patients had 619 bp deletion, 17 patients had IVS-I-1 (G→T), five patients had Cd 41/42 (-TTCT), and two patients had Cd 8/9 (+G) mutations. Fifteen haplotypes (haplotypes 1-15) were identified in 125 β-thalassemia major children. Among the five haplotypes observed in the IVS-I-5 (G→C) mutation, the H1 haplotype was most predominant with a frequency of 27.2%, followed by the H2, H4, H3, and H10 haplotypes in the given population. In 619 bp deletion, IVS-I-1 (G→T), codon 41/42, and codon 8/9, haplotype H9, H12, H11, and H5 were seen, respectively. CONCLUSION β-thalassemia was found to be the most common in the northern province of Uttar Pradesh. The linkage of β-globin gene haplotypes with β-thalassemia mutations was explored in the northern province of Uttar Pradesh. The population of different natives is being mixed up due to migration and industrialization. These were some reasons for the occurrence of haplotypic heterogeneity. This haplotype heterogeneity was correlated with the origin of these mutations found to be unlike the origin of common ones from different provinces.
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Affiliation(s)
- Nitu Nigam
- Center for Advance Research, Cytogenetics Lab, King George's Medical University, Lucknow, IND
| | - Swasti Sinha
- Hematology and Oncology/Clinical Hematology, King George's Medical University, Lucknow, IND
| | - Nishant Verma
- Pediatrics, King George's Medical University, Lucknow, IND
| | - Harish Gupta
- Medicine, King George's Medical University, Lucknow, IND
| | - Ghizal Fatima
- Public Health, Era's Lucknow Medical College and Hospital, Lucknow, IND
| | - Surbhi Gupta
- Cytogenetics Lab, King George's Medical University, Lucknow, IND
| | - Praveen Kumar
- Cytogenetics Lab, King George's Medical University, Lucknow, IND
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Seo MG, Ouh IO, Kwak D. Detection and Genotypic Analysis of Anaplasma bovis and A. phagocytophilum in Horse Blood and Lung Tissue. Int J Mol Sci 2023; 24:ijms24043239. [PMID: 36834651 PMCID: PMC9966372 DOI: 10.3390/ijms24043239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 02/10/2023] Open
Abstract
A clinical case of Anaplasma bovis was reported for the first time in our previous study (2019) in a horse, a nondefinitive host. Although A. bovis is a ruminant and not a zoonotic pathogen, it is responsible for persistent infections in horses. In this follow-up study, the prevalence of Anaplasma spp., including A. bovis, was assessed in horse blood and lung tissue samples to fully understand Anaplasma spp. pathogen distribution and the potential risk factors of infection. Among 1696 samples, including 1433 blood samples from farms nationwide and 263 lung tissue samples from horse abattoirs on Jeju Island, a total of 29 samples (1.7%) tested positive for A. bovis and 31 (1.8%) samples tested positive for A. phagocytophilum, as determined by 16S rRNA nucleotide sequencing and restriction fragment length polymorphism. This study is the first to detect A. bovis infection in horse lung tissue samples. Further studies are needed to clarify the comparison of sample types within cohorts. Although the clinical significance of Anaplasma infection was not evaluated in this study, our results emphasize the need to clarify the host tropism and genetic divergence of Anaplasma to enable the development of effective prevention and control measures through broad epidemiological studies.
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Affiliation(s)
- Min-Goo Seo
- College of Veterinary Medicine, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
| | - In-Ohk Ouh
- National Institute of Health, Korea Disease Control and Prevention Agency, 212 Osongsaengmyeong 2-ro, Cheongju, Chungbuk 28160, Republic of Korea
| | - Dongmi Kwak
- College of Veterinary Medicine, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 41566, Republic of Korea
- Correspondence: ; Tel.: +82-53-950-7794
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Alkanli N, Ay A. Investigation of the Roles of MTHFR (C677T and A1298C) and MMP-2 (-1306C>T ) Variations in Bladder Cancer Development. Turk J Urol 2023; 49:33-39. [PMID: 37877836 PMCID: PMC10081108 DOI: 10.5152/tud.2023.22185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 11/03/2022] [Indexed: 10/26/2023]
Abstract
OBJECTIVE Bladder cancer is a complex malignancy and has been associated with high morbidity. Since susceptibility to bladder cancer development differs between individuals, determining the roles of MTHFR and MMP-2 gene variations associated with this cancer is important for analyzing differences in individual susceptibility. In this study, we aimed to investigate the role of MTHFR and MMP-2 gene variations in the development of bladder cancer in the Thrace region of Turkey. MATERIALS AND METHODS One hundred seventy-nine blood samples were collected, including 98 patients with bladder cancer and 81 healthy controls. DNA extraction was carried out with blood samples. Polymerase chain reaction-restriction fragment length polymorphism was applied to detect MTHFR C677T (rs 1801133), MTHFR A1298C (rs 1801131), and MMP-2 (-1306C>T) (rs 243865) gene variants. RESULTS For the MTHFR A1298C gene variation, CC genotype was the genetic risk factor (P=.0001), while AC genotype was the protective factor (P< .0001) in the development of bladder cancer. For the MMP-2 (-1306C>T) gene variation, TT genotype (P < .0001) and T allele (P=.0006) were genetic risk factors, while AC genotype (P=.0009) was the protective factor in the development of bladder cancer. For C677T/A1298C gene variations, CC-CC combined genotype was the genetic risk factor (P=.009), while CT-AC and CC-AC combined genotypes were potential protective biomarkers (P=.013 and P < .001, respectively). CONCLUSION In our study, TT genotype and T allele were determined as genetic risk factors for MMP-2 (-1306C>T) gene variation. For C677T/A1298C gene variations, CC- CC combined genotype was detected as the genetic risk factor in the development of bladder cancer.
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Affiliation(s)
- Nevra Alkanli
- Department of Biophysics, Haliç University Faculty of Medicine, İstanbul, Turkey
| | - Arzu Ay
- Department of Biophysics, Trakya University Faculty of Medicine, Edirne, Turkey
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Futatsuya T, Anzawa K, Mochizuki T, Shimizu A. [Trichophyton tonsurans Infection]. Med Mycol J 2023; 64:49-54. [PMID: 37648498 DOI: 10.3314/mmj.23-001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Trichophyton tonsurans infection has been prevalent among individuals involved in contact sports in Japan since about 2000. The present review focuses on its diagnosis, molecular epidemiology, drug susceptibility, and infection control. The most commonly observed lesions of T. tonsurans, an anthropogenic dermatophyte, are tinea corporis and tinea capitis. However, the presence of asymptomatic carriers must be considered for infection control. Genotypic epidemiology using restriction fragment length polymorphisms (RFLP) in the non-transcribed spacer (NTS) region of the ribosomal RNA gene showed a lack of diversity of genotypes, and only the NTS I genotype is detected at present. In regard to drug susceptibility, terbinafine drug resistance has not been found to be associated with the RFLP genotypes, and it is assumed that there are no terbinafine-resistant strains in Japan. T. tonsurans coexisted with other fungi and bacteria in the scalp of asymptomatic carriers without affecting species diversity. T. tonsurans is an anthropogenic dermatophyte and may be difficult for the human immune system to eliminate. During an infection outbreak, screening of infection and treatment including asymptomatic carriers are essential to eradicate the infection.
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Affiliation(s)
- Taketoshi Futatsuya
- Department of Dermatology, Kanazawa Medical University
- Department of Dermatology, Keiju Medical Center
| | | | | | - Akira Shimizu
- Department of Dermatology, Kanazawa Medical University
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Siraj A, Yahya S, Khan A, Awan S. ACE2 Receptor Polymorphism and its Correlation with Anti-SARS-CoV-2 IgM Antibodies - A Case-Control Study. Protein Pept Lett 2023; 30:146-153. [PMID: 36475331 DOI: 10.2174/0929866530666221206094926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/01/2022] [Accepted: 10/10/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND The SARS-CoV-2 pandemic originated in Wuhan, China in December 2019 and spread rapidly worldwide. The virus gets entry into target cells via angiotensin-converting enzyme 2 (ACE2) receptors and its gene is highly polymorphic. INTRODUCTION The variations in SARS-CoV-2 susceptibility and severity can be explained on a genetic level by studying the polymorphism in ACE2 receptor polymorphism. OBJECTIVE A prospective case-control study was designed to compare the ACE2 levels in SARS-CoV- 2 patients with the healthy controls in the local population, for which a total of 100 EDTA-containing blood samples were included (50 SARS-CoV-2 IgM positive case and 50 healthy controls). METHODS PCR-RFLP was performed to investigate the polymorphism of ACE2 in genomic DNA and the ACE2 plasma levels were determined through ELISA. RESULTS No significant difference in allelic and genotype frequencies (GG, GA, AA) were observed while the ACE2 plasma levels were found to be decreased in positive samples. CONCLUSION No significant association of the ACE2 gene polymorphism (G8790A) was found with the SARS-CoV-2 susceptibility in the Pakistani population which intimates the search for other genetic factors within the local population.
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Affiliation(s)
- Anum Siraj
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), 100-Clifton Karachi, Pakistan
| | - Saira Yahya
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), 100-Clifton Karachi, Pakistan
| | - Amber Khan
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), 100-Clifton Karachi, Pakistan
| | - Saleem Awan
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), 100-Clifton Karachi, Pakistan
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Azmerin M, Hussain MS, Aziz MA, Barek MA, Begum M, Sen N, Rahman MA, Shahriar M, Baeesa SS, Ashraf GM, Islam MS. TF and TCF4 gene polymorphisms are linked to autism spectrum disorder: a case-control study. J Int Med Res 2022; 50:3000605221138492. [PMID: 36448207 PMCID: PMC9716618 DOI: 10.1177/03000605221138492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
OBJECTIVE Although the prevalence of autism spectrum disorder (ASD) is increasing, appropriate diagnosis and prevention strategies are still lacking. This case-control study was designed to explore the association between ASD and the rs1867503 and rs9951150 polymorphisms of the TF and TCF4 genes, respectively. METHODS Ninety-six children with ASD and 118 healthy children were recruited and polymerase chain reaction-restriction fragment length polymorphism technique was applied for genotyping. RESULTS The frequencies of the mutant allele G were 48% and 44% for the rs1867503 and rs9951150 polymorphisms, respectively. In our analysis, both TF and TCF4 polymorphisms were associated with an increased risk of developing ASD. AG heterozygotes (OR = 3.18), GG mutant homozygotes (OR = 2.62), AG + GG combined genotypes (OR = 2.98), and G mutant alleles of TF rs1867503 (OR = 1.94) were associated with a significantly elevated risk of ASD. Likewise, AG heterozygotes (OR = 2.92), GG mutant homozygotes (OR = 2.36), AG + GG combined genotypes (OR = 2.72), and G minor alleles of TCF4 rs9951150 (OR = 1.92) were associated with a significantly elevated risk of ASD. CONCLUSIONS Our results indicate that TF rs1867503 and TCF4 rs9951150 polymorphisms may be strongly associated with the development of ASD in Bangladeshi children.
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Affiliation(s)
- Maria Azmerin
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Md. Saddam Hussain
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh
| | - Md. Abdul Aziz
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh
| | - Md. Abdul Barek
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh
| | - Mobashera Begum
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh
| | - Niloy Sen
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh
| | - Md. Abdur Rahman
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh
| | - Mohammad Shahriar
- Department of Pharmacy, University of Asia Pacific, Dhaka, Bangladesh
| | - Saleh Salem Baeesa
- Division of Neurosurgery, College of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ghulam Md Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, University City, United Arab Emirates
| | - Mohammad Safiqul Islam
- Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh,Mohammad Safiqul Islam, Department of Pharmacy, Noakhali Science and Technology University, Sonapur-3814, Noakhali, Bangladesh.
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Wujcicka WI, Kacerovsky M, Krygier A, Krekora M, Kaczmarek P, Grzesiak M. Association of Single Nucleotide Polymorphisms from Angiogenesis-Related Genes, ANGPT2, TLR2 and TLR9, with Spontaneous Preterm Labor. Curr Issues Mol Biol 2022; 44:2939-2955. [PMID: 35877427 PMCID: PMC9322696 DOI: 10.3390/cimb44070203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 12/07/2022] Open
Abstract
In this study, we hypothesized that the changes localized at angiopoietin-2 (ANGPT2), granulocyte-macrophage colony-stimulating factor (CSF2), fms-related tyrosine kinase 1 (FLT1) and toll-like receptor (TLR) 2, TLR6 and TLR9 genes were associated with spontaneous preterm labor (PTL), as well as with possible genetic alterations on PTL-related coagulation. This case-control genetic association study aimed to identify single nucleotide polymorphisms (SNPs) for the aforementioned genes, which are correlated with genetic risk or protection against PTL in Polish women. The study was conducted in 320 patients treated between 2016 and 2020, including 160 women with PTL and 160 term controls in labor. We found that ANGPT2 rs3020221 AA homozygotes were significantly less common in PTL cases than in controls, especially after adjusting for activated partial thromboplastin time (APTT) and platelet (PLT) parameters. TC heterozygotes for TLR2 rs3804099 were associated with PTL after correcting for anemia, vaginal bleeding, and history of threatened miscarriage or PTL. TC and CC genotypes in TLR9 rs187084 were significantly less common in women with PTL, compared to the controls, after adjusting for bleeding and gestational diabetes. For the first time, it was shown that three polymorphisms-ANGPT2 rs3020221, TLR2 rs3804099 and TLR9 rs187084 -were significantly associated with PTL, adjusted by pregnancy development influencing factors.
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Affiliation(s)
- Wioletta Izabela Wujcicka
- Scientific Laboratory of the Center of Medical Laboratory Diagnostics and Screening, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland
- Correspondence: or ; Tel.: +48-42-271-15-20; Fax: +48-42-271-15-10
| | - Marian Kacerovsky
- Department of Obstetrics and Gynecology, University Hospital Hradec Kralove, Charles University, 500 03 Hradec Kralove, Czech Republic;
- Biomedical Research Center, University Hospital Hradec Kralove, 500 03 Hradec Kralove, Czech Republic
| | - Adrian Krygier
- Laboratory of Molecular Diagnostics and Pharmacogenomics, Department of Pharmaceutical Biochemistry and Molecular Diagnostics, Medical University of Lodz, 90-151 Lodz, Poland;
| | - Michał Krekora
- Department of Obstetrics and Gynecology, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland;
- Department of Gynecology and Obstetrics, Medical University of Lodz, 93-338 Lodz, Poland;
| | - Piotr Kaczmarek
- Department of Gynecology, Reproduction and Fetal Therapy, and Diagnostics and Treatment of Infertility, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland;
| | - Mariusz Grzesiak
- Department of Gynecology and Obstetrics, Medical University of Lodz, 93-338 Lodz, Poland;
- Department of Perinatology, Obstetrics and Gynecology, Polish Mother’s Memorial Hospital-Research Institute, 93-338 Lodz, Poland
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Fan J, Shen Y, Chen B, Xu C, Ye H, Wang J, Zhou W, Sheng Y, Xu F, Yang P. Lack of association between CYP11B2 -344T/C polymorphism and transient ischemic attack in a Chinese population. J Int Med Res 2021; 48:300060520947916. [PMID: 32790508 PMCID: PMC7427132 DOI: 10.1177/0300060520947916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE This study investigated whether the CYP11B2 -344T/C polymorphism is correlated with transient ischemic attack (TIA) susceptibility. METHODS We recruited 100 TIA patients and 100 control subjects and analyzed the CYP11B2 -344T/C polymorphism using restriction fragment length polymorphism (PCR-RFLP). RESULTS The frequency in TIA patients and controls was 42% compared with 48% for TT genotypes, 51% compared with 45% for TC genotypes, and 7% compared with 7% for CC genotype, respectively. Allele frequencies in TIA patients and controls were 67.5% compared with 70.5% for T-allele and 32.5% compared with 29.5% for C-allele, respectively. No association between the CYP11B2 -344T/C polymorphism and TIA was observed in all comparisons. CONCLUSION Our data suggest that there was no association between the CYP11B2 -344T/C polymorphism and TIA in a Chinese population.
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Affiliation(s)
- Jia Fan
- Changshu First People's Hospital Affiliated to Soochow University, Changshu, Jiangsu, China
| | - Yaoliang Shen
- Changshu First People's Hospital Affiliated to Soochow University, Changshu, Jiangsu, China
| | - Bo Chen
- Changshu First People's Hospital Affiliated to Soochow University, Changshu, Jiangsu, China
| | - Chunyang Xu
- Changshu First People's Hospital Affiliated to Soochow University, Changshu, Jiangsu, China
| | - Hongwei Ye
- Changshu First People's Hospital Affiliated to Soochow University, Changshu, Jiangsu, China
| | - Jian Wang
- The Fifth People's Hospital of Changshu, Changshu, Jiangsu, China
| | - Wenjun Zhou
- The Fifth People's Hospital of Changshu, Changshu, Jiangsu, China
| | - Yuefeng Sheng
- Changshu Medical Emergency Center, Changshu, Jiangsu, China
| | - Feng Xu
- Emergency Department, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Peng Yang
- Emergency Department, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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Muñoz-Calderón A, Díaz-Bello Z, Alarcón de Noya B, Noya-González OO, Schijman AG. Characterization and Follow-Up of Trypanosoma cruzi Natural Populations Refractory to Etiological Chemotherapy in Oral Chagas Disease Patients. Front Cell Infect Microbiol 2021; 11:665063. [PMID: 33996636 PMCID: PMC8121101 DOI: 10.3389/fcimb.2021.665063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
We aimed to characterize the genetic constitution of natural T. cruzi populations involved in an Oral Chagas Disease (OCD) outbreak at a rural school of the community of Chichiriviche de la Costa, Venezuela, which affected patients did not respond to the etiological treatment. Peripheral blood samples and/or hemocultures were obtained from twenty-nine OCD patients at time of diagnosis or along nine years of Post-treatment (Tx) follow-up. The IgG serology, T. cruzi discrete typing units (DTU), satellite DNA-qPCR parasitic loads, and minicircle signatures were determined at Pre-Tx and after Tx. The serological titles and parasitic loads changed after treatment, with a significant decrease of IgG titers (Spearman’s r value= -0.961) and median parasite loads from 2.869 [IQR = 2.113 to 3.720] to 0.105 [IQR = -1.147 to 1.761] log10 par eq. /mL at Pre-Tx and Post-Tx, respectively, suggesting infection evolution from acute to chronic phase, without seroconversion or parasitological eradication, which was indicative of treatment failure. All patients were infected with T. cruzi DTU I populations. At Pre-Tx their median Jaccard genetic distances were 0.775 [IQR = 0.708 to 0.882], decreasing in genetic variability towards the end of follow-up (Mann-Whitney U test p= 0.0031). Interestingly, no Post-Tx minicircle signature was identical to its Pre-Tx counterpart population in a same patient, revealing selection of parasite subpopulations between the primary infection and Post-Tx. The parasitic populations isolated from hemocultures showed a lower number of bands in the minicircle signatures with respect to the signatures obtained directly from the patients’ blood samples, demonstrating a process of parasitic selection and reduction of the population variability that initially infected the patients. Decrease of parasitic loads after treatment as well as Pre- and Post-Tx intra-TcI diversity might be a consequence of both, natural evolution of the acute infection to the chronic phase and persistence of refractory populations due to Tx selection.
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Affiliation(s)
- Arturo Muñoz-Calderón
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Zoraida Díaz-Bello
- Instituto de Medicina Tropical "Dr Félix Pifano", Universidad Central de Venezuela, Caracas, Venezuela
| | | | - Oscar O Noya-González
- Instituto de Medicina Tropical "Dr Félix Pifano", Universidad Central de Venezuela, Caracas, Venezuela
| | - Alejandro G Schijman
- Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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12
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Seyedian SM, Bijanzadeh M, Ahmadi F, Haghighizadeh MH. Association between Endothelial nitric oxide synthase and Hepatic lipase gene polymorphisms with the risk of coronary artery disease in Southern Iran population - A case control study. Nucleosides Nucleotides Nucleic Acids 2021; 40:423-433. [PMID: 33673789 DOI: 10.1080/15257770.2021.1892130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Coronary artery disease is a multifactorial genetic disease caused by the interaction between genetic and environmental factors. Angiography is the gold standard method for the diagnosis and determining the stage of cardiac disorder. The rs1800588 at the Hepatic Lipase gene and rs1799983 at the endothelial nitric oxide synthase (eNOS) gene are two candidate SNP that result in increased risk of this disease. The aim of this study was to find out the associations of the two mentioned polymorphisms with angiographically proven coronary artery patients in a southern Iranian population. In this study, this two polymorphisms in 287 patients and 229 matched controls were confirmed by angiography and analyzed. Genotype analysis was carried out by PCR and RFLP. Data showed that a significant difference for the eNOS gene polymorphism (p = 0.004) and a non-significant difference for the Hepatic lipase polymorphism (p = 0.261) and increasing severity of angiographic evidences of coronary artery disease were observed. Conclusively the significant association of the G894T with the narrowing of two or three coronary vessels of this patients in an Iranian population have been detected.
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Affiliation(s)
- Seyed Masoud Seyedian
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Cardiology, Golestan Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahdi Bijanzadeh
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Medical genetics, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Farzaneh Ahmadi
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of Cardiology, Golestan Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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13
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Mashhadi MA, Arbabi N, Sepehri Rad N, Sargazi S, Harati-Sadegh M. Association between common variants in vitamin D receptor gene and susceptibility to Non-Hodgkin's lymphoma: a case-control study. Nucleosides Nucleotides Nucleic Acids 2021; 40:288-299. [PMID: 33446057 DOI: 10.1080/15257770.2020.1871488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Vitamin D (VDR)-mediated signaling contributes to the cell signaling pathways that affect cancer development. This study is conducted on 104 patients diagnosed with non-Hodgkin's lymphoma (NHL) and 246 healthy subjects to investigate the link between five genetic variants spanning the VDR gene and the risk of this malignancy in Iranian subjects. The PCR-RFLP method was used for the analysis of BsmI (rs1544410), ApaI (rs7975232), FokI (rs2228570) and TaqI (rs731236) variants. A simple Tetra-ARMS-PCR technique was employed for the genotyping of the Cdx2 (rs11568820) variant. No significant link was found between both groups regarding ApaI (rs7975232) and FokI (rs2228570) variants (P > 0.05). Also, different genetic models of TaqI (rs731236), BsmI (rs1544410) and Cdx2 (rs11568820) polymorphisms were significantly correlated to decreased risk of NHL (Odd ratios <1). We found three haplotypes were strongly associated with an increased risk of NHL (P < 0.0001). Linkage-disequilibrium (LD) analysis showed a strong linkage between TaqI (rs731236) and BsmI (rs1544410) among NHL case and control subjects. Our findings indicated that functional variants of the VDR gene are linked to a decreased risk of NHL in our population. Further replication studies in different ethnic groups are needed to validate our results.
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Affiliation(s)
- Mohammad Ali Mashhadi
- Department of Internal Medicine, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Narges Arbabi
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Nahid Sepehri Rad
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Harati-Sadegh
- Genetic of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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Shekarriz R, Alikhani R, Ghasemi M, Navaei RA, Hashemi-Soteh MB. Correlation of -160C > A and -347GA > G polymorphisms in E-cadherin gene and gastric cancer in north of Iran. J Res Med Sci 2021; 26:3. [PMID: 34084182 PMCID: PMC8103955 DOI: 10.4103/jrms.jrms_50_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/26/2020] [Accepted: 08/31/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND E-cadherin (CDH1 gene) is a protein involved in cell-cell adhesion. There are reports on the association of -160C > A (rs16260) and -347GA > G (rs5030625) polymorphisms in the 5'-promoter region of the CDH1 gene with tumor development and progression of gastric cancer. This study aimed to examine the potential relationship between these two polymorphisms and gastric cancer in patients from Mazandaran province, Northern Iran. MATERIALS AND METHODS A case-control study was conducted to test 97 patients and 95 healthy controls. Genomic DNA was extracted from peripheral blood followed by polymerase chain reaction amplification. Genotyping analysis was carried out using restriction fragment length polymorphism analysis for two potentially functional polymorphisms. RESULTS Heterozygous genotype GA/G versus GA/GA of rs5030625 (-347 GA > G) was found to be associated with increased risk of gastric cancer in the people studied (odds ratio = 5.73, 95% confidence interval = 2.11-15.56, P = 0.001). Furthermore, AA or CA genotype in -160C > A polymorphism did not show any increased risk of gastric cancer (P = 0.559). CONCLUSION The present study revealed that GA/G genotype of rs5030625 (-347 GA > G) polymorphism is associated with gastric cancer in Northern Iran.
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Affiliation(s)
- Ramin Shekarriz
- Department of Hematology and Oncology, Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Alikhani
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohaddeseh Ghasemi
- Department of Internal Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Reza Alizadeh Navaei
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mohammad Bagher Hashemi-Soteh
- Immunogenetic Research Center, Cell and Molecular Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Address for correspondence: Dr. Mohammad Bagher Hashemi-Soteh, Immunogenetic Research Center, Cell and Molecular Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran. E-mail:
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Abharian PH, Dehghan P, Hassani-Abharian P, Jabalameli Z. Frequency of Candida Species in the Oral Cavity of Narcotics and Stimulants Smokers in Isfahan, Using Polymerase Chain Reaction- Restriction Fragment Length Polymorphism Method. Adv Biomed Res 2020; 9:30. [PMID: 33072642 PMCID: PMC7532823 DOI: 10.4103/abr.abr_38_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/29/2020] [Accepted: 05/11/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Candida species are a group of coexistent microorganisms in the oral cavity that opportunistically cause disease in vulnerable people, including addicts. This study is aimed at identifying and determining the frequency of Candida species in the oral cavity of the addicts to inform the epidemiological panel and to warn to prevent the resistance of the species. Materials and Methods: In this study, sampling was done from the oral cavity of 83 addicts who referred to Addiction Treatment Centers in Isfahan, Iran, using moist sterile swab. The presence of yeast on the direct microscope slides of 58 samples was confirmed. To carry out culture and the primary identification, Sabouraud dextrose agar medium with chloramphenicol as well as HiCrome Candida agar medium was used. Isolates were identified by polymerase chain reaction (PCR) restriction fragment length polymorphism (using specific primers ITS1-ITS4 and MSP I enzyme) and Duplex PCR test (using specific primers CDU1-CDU2/CAL1-CAL2). Results: Out of 93 Candida isolates which had been isolated from 58 culture-positive samples of the oral cavity, Candida albicans (41.93%) were the most prevalent species, followed by Candida dubliniensis (24.73%), Candida glabrata (21.50%), Candida kefyr (8.60%), Candida tropicalis (2.15%), and Candida parapsilosis (1.07%), respectively. In 33 cases (56.90%), the presence of more than one Candida species was observed. Conclusion: Compared to the studies conducted on the oral cavity of healthy controls, smoking certain drugs can have a significant effect on the presence and frequency of Candida species, particularly C. dubliniensis and C. glabrata.
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Affiliation(s)
- Parastoo Hassani Abharian
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Parvin Dehghan
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Peyman Hassani-Abharian
- Department of Cognitive Rehabilitation, Brain and Cognition Clinic, Institute for Cognitive Science Studies, Tehran, Iran
| | - Zahra Jabalameli
- Department of Laboratory Sciences, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat, Iran.,Health Sciences Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
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Suresh M, Skariyachan S, Narayanan N, Pullampara Rajamma J, Panickassery Ramakrishnan MK. Mutational Variation Analysis of oprD Porin Gene in Multidrug-Resistant Clinical Isolates of Pseudomonas aeruginosa. Microb Drug Resist 2020; 26:869-879. [PMID: 32083512 DOI: 10.1089/mdr.2019.0147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The present study deals with the outer membrane OprD porin protein in 29 clinical bacterial isolates of multidrug-resistant Pseudomonas aeruginosa. oprD porin gene expression was investigated using real-time reverse transcription-PCR. Amplicons from oprD and its transcriptional regulator mexT gene were sequenced and analyzed for mutations. Hypothetical models of selected mutant OprD-porin proteins were predicted and refined by homology modeling approach. oprD ampliconic sequences were also screened for restriction fragment length polymorphism (RFLP). The oprD gene was found to be downregulated in 89.7% (n = 26) of the isolates in comparison to the transcript levels in the reference strain P. aeruginosa-PAO (MTCC-3541). Interestingly, all these isolates displayed the presence of a conspicuous 8-bp deletion (GGCCAGCC) at nucleotide position 235 of mexT regulatory gene. Based on the mutational patterns observed in oprD gene, the isolates were classified into categories designated as A, B1-2, C1-4, D1-6, E1-2, and F. Our hypothetical models revealed that mutations were predominantly confined to the extracellular loops emanating from the β-barrel porin protein. These protein models also enabled clear visualization of loss of substantial portions of the truncated polypeptide. Incidentally, since most of the oprD amplicons of the clinical isolates were found to display distinct RFLP banding patterns, our results also provide a useful diagnostic tool for detection of P. aeruginosa porin mutants.
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Affiliation(s)
- Manju Suresh
- Department of Biotechnology, University of Calicut, Malappuram, India
| | | | - Nithya Narayanan
- Department of Biotechnology, University of Calicut, Malappuram, India
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Nithya K, Parameswari B, Viswanathan R. Mixed Infection of Sugarcane Yellow Leaf Virus and Grassy Shoot Phytoplasma in Yellow Leaf Affected Indian Sugarcane Cultivars. Plant Pathol J 2020; 36:364-377. [PMID: 32788895 PMCID: PMC7403522 DOI: 10.5423/ppj.oa.06.2020.0092] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/17/2020] [Accepted: 06/25/2020] [Indexed: 02/08/2023]
Abstract
Sugarcane is an important sugar crop contributes more than 80% of world sugar production. Mosaic, leaf fleck, and yellow leaf (YL) are the major viral diseases affecting sugarcane, amongst YL occurrence is widely reported in all the sugarcane growing countries. It is caused by Sugarcane yellow leaf virus (SCYLV) and detailed works were done on complete genome characterization, transmission, and management. However, in countries like Egypt, South Africa, Cuba, Mauritius and Hawaii, the disease was reported to the cause of sugarcane yellow leaf phytoplasma (SCYP) and/or SCYLV as single/combined infections. Hence, we have investigated in detail to identify the exact Candidatus phytoplasma taxon associated in Indian cultivars affected with YL. The sequencing results and the restriction fragment length polymorphism pattern of the PCR products using the universal phytoplasma primers confirmed presence of sugarcane grassy shoot (SCGS) phytoplasma (16SrXI group) in the YL-affected plants. Mixed infection of SCYLV and SCGS phytoplasma was estimated as 32.8% in YL affected plants. Evolutionary genetic relationship between SCYP and SCGS phytoplasma representatively taken from different countries showed that SCYP from South Africa and Cuba were diverged from others and had a highest similarity with SCGS phytoplasma. Although we wanted to identify SCYP from YL affected Indian sugarcane cultivars, the study clearly indicated a clear absence of SCYP in YL affected plants and we found SCYLV as the primary cause for the disease.
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Affiliation(s)
- Kadirvel Nithya
- ICAR-Sugarcane Breeding Institute, Coimbatore 641 007, Tamil Nadu, India
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Baghdadi I, Abu Ella K, El Shaaraway A, Elshayeb E, El-Rebey HS, El Hoseeny M, Naguib M, Nada A. Genetic Polymorphism of Epidermal Growth Factor Gene as a Predictor of Hepatocellular Carcinoma in Hepatitis C Cirrhotic Patients. Asian Pac J Cancer Prev 2020; 21:2047-2053. [PMID: 32711431 PMCID: PMC7573408 DOI: 10.31557/apjcp.2020.21.7.2047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Indexed: 01/27/2023] Open
Abstract
Background: In Egypt, the incidence of hepatocellular carcinoma (HCC) is approximately 4.7% of chronic liver disease patients due to (HCV) infection. Epidermal growth factor (EGF) plays an important role in hepatocyte regeneration. A functional polymorphism in EGF 61A>G was identified; itwas associated with higher risk of HCC. Objectives: to investigate the correlation between the epidermal growth factor (EGF) polymorphism and the risk of hepatocellular carcinoma (HCC) in hepatitis C viral (HCV) cirrhotic patients as well as its relation to EGF protein expression in HCC tissue. Patients and methods: this casecontrol study was conducted on 75 HCV cirrhotic patients including 50 HCC patients (25 withresectable HCC and 25 with advanced unresectable HCC) and 25 healthy persons were included. EGF genotype was detected by restriction fragment length polymorphism. EGF expression in HCC tissue biopsiesfrom patientswhounderwent surgical resection was done by immunohistochemical examination. Results: The GG genotype was associated with significant increased risk of HCC compared to AA genotypes (P=0.031) in cirrhotic group. The G allele had a highly significant risk of HCC compared to allele Ain recessive model GG vs. AG+AA (P=0.036) rather than in the dominant model GG +AG vs. AA (P=0.66). There was significant increased expression of EGF in tumour tissues in patients with GG genotype compared to AG genotype and AA genotype p= 0.019. Conclusion: EGF gene polymorphism (GG genotype) had a significant risk of HCC development in cirrhotic patients. This is confirmed by increased EGF expression in liver tumor tissue from HCC patients.
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Affiliation(s)
- Ibrahim Baghdadi
- Internal Medicine Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Khaled Abu Ella
- Liver and Hepatobiliary surgery Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Ahmed El Shaaraway
- Clinical Pathology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Elsayed Elshayeb
- Internal Medicine Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Hala S El-Rebey
- Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Mohamed El Hoseeny
- Hepatology Department, Mahlla teaching liver hospital, El Mahlla, Gharbeya, Egypt
| | - Mary Naguib
- Clinical Pathology Department, National Liver Institute, Menoufia University, Menoufia, Egypt
| | - Ali Nada
- Hepatology Gastroenterology Department, National Liver Institute, Menofia University. Egypt
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Hosseini SM, Mohammadiasl J, Talaiezadeh A, Alidadi R, Bijanzadeh M. Influence of Two DNA Repair Pathway Polymorphisms in Colorectal Cancer Risk in Southwest Iran. Asian Pac J Cancer Prev 2020; 21:1919-1924. [PMID: 32711416 PMCID: PMC7573413 DOI: 10.31557/apjcp.2020.21.7.1919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Indexed: 11/25/2022] Open
Abstract
Objective: X-ray cross-complementing group 1 (XRCC1) and 8 Oxo guanine DNA-glycosylase 1 (OGG1) genes are implicated in the repair of single-stranded breaks (SSBRs) and base excision repair (BER) pathways. Common polymorphisms in DNA repair genes are supposed to decrease the capability of DNA repair and cause genetic instability. This study was designed to investigate the association between XRCC1 (rs25487) and OGG1 (rs1052133) polymorphisms and susceptibility to colorectal cancer (CRC) in the Ahvaz city, south-west Iran. Methods: This case- control study comprised 150 patients and 150 controls that were selected from 2 educational hospitals in Ahvaz. They were matched for age and gender, and their genotyping was carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results: Our results indicate that the frequency of the Gln (A) allele of XRCC1 (rs25487) is significantly higher in colorectal cancer patients, compare to controls (p = 0.01, OR: 1.54, 95% CI 1.9–13.3). Significant increased risk of cancer was observed in XRCC1 (rs25487) genotypes (p = 0.001 OR: 5.3, 95% CI 1.9–14.2 for Gln / Gln), while no association was found between OGG1 (rs1052133) and colorectal cancer risk (p = 0.6). Conclusion: Our study suggests that XRCC1 (rs25487) polymorphism might be associated with an increasing risk of CRC in Ahvaz. It also demonstrates positive correlation between the XRCC1 (rs25487) genotypes and demographic characteristics, such as smoking and increased age in patients and control groups.
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Affiliation(s)
- Seyed Mohammad Hosseini
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Javad Mohammadiasl
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Abdulhasan Talaiezadeh
- Cancer, Environmental and Petroleum Pollutants Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Department of General Surgery, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Rahim Alidadi
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mahdi Bijanzadeh
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.,Cancer, Environmental and Petroleum Pollutants Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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20
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Verma S, Sharma V, Nagpal A, Bhat A, Bhat GR, Shah R, Wakhloo A, Suri J, Abrol D, Kaul S, Bhat A, Verma V, Kumar R. DNA base excision repair genes variants rs25487 (X-ray repair cross-complementing 1) and rs1052133 (human 8-oxoguanine glycosylase 1) with susceptibility to ovarian cancer in the population of the Jammu region, India. J Cancer Res Ther 2020; 15:1270-1275. [PMID: 31898659 DOI: 10.4103/jcrt.jcrt_65_18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Ovarian cancer is highly prevalent in the population of Jammu, in India; the ovarian cancer ranks third among other types of cancer prevalent in females. However, association studies on ovarian cancer are lacking in this region. We aimed to investigate the disease susceptible variants rs1052133 (human 8-oxoguanine glycosylase 1 [hOGG1]) and rs25487 (X-ray repair cross-complementing 1 [XRCC1]) with ovarian cancer in population of Jammu, India. Materials and Methods The study conducted in the Shri Mata Vaishno Devi University is a 3-year study which included a total of 280 well-characterized samples (130 ovarian cancer cases and 150 healthy controls). hOGG1 and XRCC1 polymorphisms were determined by polymerase chain reaction-based restriction fragment length polymorphism, and these genotyping results were confirmed by Sanger sequencing. Hardy-Weinberg equilibrium for both single-nucleotide polymorphisms (SNPs) was assessed using the Chi-square test. The allele and genotype-specific risks were estimated by odds ratios with 95% confidence intervals. Results In this preliminary study, SNP rs1052133 showed protection with ovarian cancer (P = 0.042). The SNP rs25487 was not found associated with ovarian cancer (P = 0.271). Conclusion Our results indicate that the G allele of rs1052133 imparts protection to the population whereas variant rs25487 was not associated with ovarian cancer in population from the Jammu region, indicating that larger sample size is needed for further statistical validation. Further, association of other SNPs in these genes should also be carried out as their role cannot be ruled out.
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Affiliation(s)
- Sonali Verma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Varun Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Ashna Nagpal
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Amrita Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - G R Bhat
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Ruchi Shah
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Ajay Wakhloo
- Department of Obstetrics and Gynecology, Government Medical College, Jammu, Jammu and Kashmir, India
| | - Jyotsna Suri
- Department of Pathology, Government Medical College, Jammu, Jammu and Kashmir, India
| | - Deepak Abrol
- Department of Radiotherapy, Government Medical College, Jammu, Jammu and Kashmir, India
| | - Sandeep Kaul
- Shri Mata Vaishno Devi Narayana Superspeciality Hospital, Katra, Jammu and Kashmir, India
| | - Audesh Bhat
- Centre for Molecular Biology, Central University, Jammu, Jammu and Kashmir, India
| | - Vijeshwar Verma
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, India
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21
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Chakravarti A, Bharara T, Kapoor N, Ashraf A. Levels of 25-hydroxy Vitamin D3 and Vitamin D Receptor Polymorphism in Severe Dengue Cases from New Delhi. Trop Med Infect Dis 2020; 5:tropicalmed5020072. [PMID: 32375246 PMCID: PMC7344752 DOI: 10.3390/tropicalmed5020072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Dengue is the "phoenix" that never went to ashes. First identified in 1943, in Japan, dengue virus has worldwide distribution and is a grave public health concern in developing countries like India; Methods: A cross sectional study was conducted among adults suspected of having dengue fever and attending Lok Nayak Hospital, New Delhi. Restriction Fragment Length Polymorphism was completed for the detection of vitamin D receptor (VDR) gene polymorphism; Results: Serum 25-hydroxy vitamin D3 (vitamin D) levels were found to be 1.6 times elevated in severe dengue cases as compared to healthy controls. Vitamin D levels were significantly higher in secondary infections compared to primary infections as well as secondary severe dengue cases as compared to secondary non-severe cases (p value < 0.05). A significant association of the T allele (rs2228570) was seen in severe dengue cases, while, when comparing the A/A with A/C and C/C genotypes (rs7975232) among dengue cases and healthy controls, the odds ratio was estimated to be 1.24 (0.55-2.75, p > 0.05) and 0.28 (0.08-0.96, p < 0.05) respectively; Conclusions: The present study is an attempt at decoding the role of vitamin D in dengue disease pathogenesis and exploring the role of genetic polymorphism in dengue disease pathogenesis.
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Affiliation(s)
- Anita Chakravarti
- Department of Microbiology, Shree Guru Gobind Singh Tricentenary University, Gurugram (Haryana) 1222505, India;
- Correspondence:
| | - Tanisha Bharara
- Department of Microbiology, Shree Guru Gobind Singh Tricentenary University, Gurugram (Haryana) 1222505, India;
| | - Neeru Kapoor
- Department of Microbiology, Maulana Azad Medical College, New Delhi 110002, India; (N.K.); (A.A.)
| | - Anzar Ashraf
- Department of Microbiology, Maulana Azad Medical College, New Delhi 110002, India; (N.K.); (A.A.)
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Kumar BS, Narayana HI, Murthy BVS, Mathew S, Damodhar P, Kumar SSS. Isolation and genetic characterization of mutans streptococci associated with dental caries in rural field practice of a dental institution: In vivo study. Indian J Dent Res 2020; 30:889-893. [PMID: 31939366 DOI: 10.4103/ijdr.ijdr_269_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Streptococcus mutans is well-known causative microorganism in the development of dental caries because they drop the plaque pH and produce acids from carbohydrates and survive in the acidic environment. It is now evident that knowledge of the bacteria enforces empirical approach to therapy, then specific antimicrobial therapy that might allow more conservative treatment options. Over the past few decades, there has been a remarkable increase in the prevalence rate of dental caries among children and the elders. Genotypic methods help in the detection and manipulation of nucleic acids which allows microbial genes to be examined directly. Aim The aim of this study is to isolate and characterize S. mutans from rural population and to obtain genomic DNA and screen DNA band pattern. Methodology A total of 80 plaque samples were collected from the buccal surfaces of maxillary and lingual surfaces of mandibular first molar with carious teeth in patients at a rural outreach center in Chikkaballapur district, Karnataka. Among these, 48 clinical isolates of S. mutans were recovered. Further, genomic DNA was extracted from all the positively isolated strains including the standard strain (microbial type culture collection 497), and stored at 4°C in tris EDTA buffer (TE). To analyze the molecular heterogeneity of the clinical strains, polymerase chain reaction (PCR), and restriction fragment length polymorphism was performed using restriction enzymes Hind III and Hae III. Using agarose gel electrophoresis, genomic DNA band pattern was analyzed. Results Statistically significant difference was seen in the "dex" gene collected from sample DNA and standard DNA in three different parameters (S. mutans 497). Conclusion Genomic DNA of S. mutans was successfully isolated from the rural population. Dex gene was successfully amplified using PCR. Hae III enzymes successfully digested PCR amplicons and the fragments exhibited visible heterogeneity.
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Affiliation(s)
- B Santosh Kumar
- Department of Conservative Dentistry and Endodontics, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - H Indiresha Narayana
- Department of Conservative Dentistry and Endodontics, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - B V Sreenivasa Murthy
- Department of Conservative Dentistry and Endodontics, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - Sylvia Mathew
- Department of Conservative Dentistry and Endodontics, Faculty of Dental Sciences, Ramaiah University of Applied Sciences, Bengaluru, Karnataka, India
| | - P Damodhar
- Department of Biotechnology, MSRIT, Bengaluru, Karnataka, India
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Polat PF, Şahan A, Aksoy G, Timurkan MO, Dinçer E. Molecular and restriction fragment length polymorphism analysis of canine parvovirus 2 (CPV-2) in dogs in southeast Anatolia, Turkey. ACTA ACUST UNITED AC 2019; 86:e1-e8. [PMID: 31478735 PMCID: PMC6739549 DOI: 10.4102/ojvr.v86i1.1734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 11/04/2022]
Abstract
Canine parvovirus-2 (CPV-2) is the aetiological agent of an infectious viral disease of dogs, characterised by diarrhoea and vomiting. Mutations of the CPV-2 genome have generated new variants circulating worldwide. This article reports the molecular analysis of CPV-2 variants collected in the dog population in southeast Anatolia, Turkey. Twenty blood samples previously taken for the laboratory diagnosis of dogs with suspected parvovirus were screened for CPV-2 by polymerase chain reaction (PCR). Of the 20 samples, 18 tested positive for CPV-2. Partial VP2 gene sequencing and restriction fragment length polymorphism (RFLP) analysis revealed CPV-2a (n = 1), CPV-2b (n = 16) and CPV-2c (n = 1) variants. Phylogenetic analysis based on the partial length VP2 gene showed that CPV-2b (n = 15) variants showed sequences clustering separately in the phylogenetic tree. The CPV-2c sample was phylogenetically related to Chinese strains and Indonesia strain, whereas the CPV-2a sample was phylogenetically related to the Portuguese strain. These results, which are the first to demonstrate the presence of CPV-2c in the dog population of southeast Anatolia, Turkey, indicate that CPV-2a/2b/2c variants co-exist in Turkey’s dog population.
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Affiliation(s)
- Pelin F Polat
- Department of Internal Medicine, Faculty of Veterinary Medicine, Harran University, Sanliurfa.
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Coates BS, Abel CA. Differentiation of European Corn Borer (Lepidoptera: Crambidae) and American Lotus Borer (Lepidoptera: Crambidae), Ostrinia penitalis, from North American Field Collections. J Econ Entomol 2019; 112:2007-2011. [PMID: 31321434 DOI: 10.1093/jee/toz078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Indexed: 06/10/2023]
Abstract
The European corn borer, Ostrinia nubilalis (Lepidoptera: Crambidae), is a perennial insect pest of cultivated maize that was inadvertently introduced into North America in the early 1900s, but population densities have decreased since the widespread adoption of transgenic hybrids that express Bacillus thuringiensis (Bt) toxins. The native American lotus borer, Ostrinia penitalis (Lepidoptera: Crambidae), is among the most ancestral species described in the genus Ostrinia, and has a geographic range that coincides with that of O. nubilalis across major maize growing regions of North America. Due to the recent decrease in O. nubilalis populations, O. penitalis has become more pronounced in light trap samples intended to monitor O. nubilalis. A molecular tool based on variation in restriction endonuclease digestion pattern of a polymerase chain reaction amplified fragment of the mitochondrial cytochrome c oxidase subunit I (coxI) gene was developed and validated to differentiate these two species. This method was applied to light trap samples over a 2-yr period and achieved accurate quantification of species, and shows that O. penitalis can be prevalent in O. nubilalis first flight sampling. These methods are useful for contemporary O. nubilalis field research in North America.
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Affiliation(s)
- Brad S Coates
- Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, Ames, IA
| | - Craig A Abel
- Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, Ames, IA
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MONTAZERI-NAJAFABADY N, DABBAGHMANESH MH, MOHAMMADIAN AMIRI R, BAKHSHAYESHKARAM M, RANJBAR OMRANI G. Influence of LRP5 (rs556442) polymorphism on insulin resistance in healthy Iranian
children and adolescents. Turk J Med Sci 2019; 49:490-496. [PMID: 30866603 PMCID: PMC7018221 DOI: 10.3906/sag-1809-107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background/aim Genetic aspects play a role in insulin resistance in children. In this study, for the first time, the association of LRP5 (rs556442) polymorphism and insulin resistance in Iranian children and adolescents was investigated. Materials and methods The study population comprises children and adolescents aged 9–18 years. Anthropometric and biochemical parameters were assessed. Insulin resistance/sensitivity was determined by the quantitative insulin sensitivity check index (QUICKI), homeostasis model assessment-insulin resistance (HOMA-IR), insulin-to-glucose ratio, McAuley index, revised McAuley index, fasting insulin resistance index (FIRI), and Bennett’s index. LRP5 (rs566442) single nucleotide polymorphism (SNP) was identified using restriction fragment length polymorphism (RFLP). Linear regression analysis was used to determine the association between the LRP5 polymorphism (rs556442) and insulin sensitivity indexes. Results Significant differences were found between GG genotype vs. AG/AA genotypes for McAuley index (P = 0.049) and revised McAuley index (P = 0.044) when adjusted for interaction factors (age, sex, and puberty) in regression models. No significant association was found between LRP5 (rs566442) and other insulin resistance indexes. Also, LRP5 (rs566442) did not show a significant impact on biochemical parameters. Conclusion This study showed that LRP5 polymorphism (rs556442) was associated with insulin resistance in Iranian children and adolescents.
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Affiliation(s)
- Nima MONTAZERI-NAJAFABADY
- Endocrinology and Metabolism Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, ShirazIran
| | - Mohammad Hossein DABBAGHMANESH
- Endocrinology and Metabolism Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, ShirazIran
- * To whom correspondence should be addressed. E-mail:
| | - Rajeeh MOHAMMADIAN AMIRI
- Endocrinology and Metabolism Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, ShirazIran
| | | | - Gholamhossein RANJBAR OMRANI
- Endocrinology and Metabolism Research Center, Nemazee Hospital, Shiraz University of Medical Sciences, ShirazIran
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Izzo SA, Quintana S, Espinosa M, Babay PA, Peressutti SR. First Characterization of PAH-degrading bacteria from Río de la Plata and high-resolution melting: an encouraging step toward bioremediation. Environ Technol 2019; 40:1250-1261. [PMID: 29261428 DOI: 10.1080/09593330.2017.1420104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/18/2017] [Indexed: 06/07/2023]
Abstract
The Río de la Plata, one of the most important estuarine environments in South America that sustains valuable fisheries, is affected by PAH contamination associated with oil industry and port activities. A total of 95 bacteria with potential to degrade phenanthrene were obtained from water samples using traditional culture methods. PCR-RFLP analysis of 16S rDNA partial fragments was used as a screening tool for reducing the number of isolates during diversity studies, obtaining 42 strains with different fingerprint patterns. Phylogenetic analysis indicated that they were affiliated to 19 different genera of Gamma- and Alpha-Proteobacteria, and Actinobacteria. Some of them showed an efficient phenanthrene degradation by HPLC (between 83% and 97%) and surfactant production (between 40% and 55%). They could be an alternative for microbial selection in the degradation of PAHs in this estuarine system. In order to detect and monitor PAH-degrading bacteria in this highly productive area, rDNA amplicons of the 33 isolates, produced by PCR real time, were tested by the high-resolution melting (HRM) technique. After analyzing the generated melting curves, it was possible to accurately distinguish nine patterns corresponding to eight different genera. HRM analysis allowed a differentiation at the species level for genera Pseudomonas, Halomonas and Vibrio. The implementation of this method as a fast and sensitive scanning approach to identify PAH-degrading bacteria, avoiding the sequencing step, would mean an advance in bioremediation technologies.
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Affiliation(s)
- Silvina A Izzo
- a Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP) , Mar del Plata, Buenos Aires , Argentina
| | - Silvina Quintana
- b Área de Biología Molecular de Fares Taie , Instituto de Análisis , Rivadavia, Mar del Plata , Argentina
- c Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Buenos Aires , Argentina
| | - Mariela Espinosa
- d Comisión Nacional de Energía Atómica , Buenos Aires , Argentina
| | - Paola A Babay
- d Comisión Nacional de Energía Atómica , Buenos Aires , Argentina
| | - Silvia R Peressutti
- a Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP) , Mar del Plata, Buenos Aires , Argentina
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Seo MG, Ouh IO, Choi E, Kwon OD, Kwak D. Molecular Detection and Phylogenetic Analysis of Anaplasma phagocytophilum in Horses in Korea. Korean J Parasitol 2018; 56:559-565. [PMID: 30630276 PMCID: PMC6327205 DOI: 10.3347/kjp.2018.56.6.559] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/14/2018] [Indexed: 01/18/2023]
Abstract
The identification and characterization of pathogenic and zoonotic tick-borne diseases like granulocytic anaplasmosis are essential for developing effective control programs. The differential diagnosis of pathogenic Anaplasma phagocytophilum and non-pathogenic A. phagocytophilum-like Anaplasma spp. is important for implementing effective treatment from control programs. The objective of the present study was to investigate the prevalence of Anaplasma spp. in horses in Korea by nucleotide sequencing and restriction enzyme fragment length polymorphism assay. Of the 627 horses included in the study, only 1 (0.2%) was infected with A. phagocytophilum. Co-infection with A. phagocytophilumlike Anaplasma spp. was not detected in the study. The 16S rRNA sequence of A. phagocytophilum was similar (99.5–100%) to A. phagocytophilum 16S rRNA isolated from horses in other countries. PCR adapted to amplify A. phagocytophilum groEL and msp2 genes failed to generate amplicons, suggesting genetic diversity in these genes. This study is the first molecular detection of A. phagocytophilum in horses in Korea. Human granulocytic anaplasmosis and animal infection of A. phagocytophilum have been reported in Korea recently. Because of vector tick distribution, global warming, and the increase of the horse industry, horses should be considered as a potential reservoir for A. phagocytophilum, and cross infectivity should be evaluated even though a low prevalence of infection was detected in this study. Furthermore, continuous surveillance and effective control measures for A. phagocytophilum should be established to prevent disease distribution and possible transmission to humans.
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Affiliation(s)
- Min-Goo Seo
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea.,Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - In-Ohk Ouh
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | | | - Oh-Deog Kwon
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Dongmi Kwak
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea.,Cardiovascular Research Institute, Kyungpook National University, Daegu 41944, Korea
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Worasilchai N, Chaumpluk P, Chakrabarti A, Chindamporn A. Differential diagnosis for pythiosis using thermophilic helicase DNA amplification and restriction fragment length polymorphism (tHDA-RFLP). Med Mycol 2018; 56:216-224. [PMID: 28525598 DOI: 10.1093/mmy/myx033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 04/03/2017] [Indexed: 11/13/2022] Open
Abstract
Pythiosis is caused by Pythium insidiosum, a fungus-like microbe belonging to the kingdom Stramenopila. Its diagnosis is challenging due to clinical and histopathological similarities with the fungal microbes that cause mucormycosis and entomophthoramycosis. In addition, the proper identification of P. insidiosum in the clinical laboratory is difficult. We have developed a rapid and accurate, species-specific identification method using a thermophilic helicase DNA amplification (tHDA) technique, to differentiate this pathogen from closely related pathogenic fungi. Sixty-seven fungal isolates, including 39 of P. insidiosum, were evaluated. A 91 base-pair (bp) DNA fragment was consistently amplified using a COX2 primer. The limiting concentrations of the one- and two-step tHDA protocols were 100 picograms (1.74 × 102 copies) and 100 femtograms (1.74 × 10-1 copies), respectively. The CviKI-1 enzyme in restriction fragment length polymorphism (RFLP) with the 91 bp amplicons accurately separated P. insidiosum from other fungal species. The data suggest that this tHDA-RFLP assay is a rapid and accurate test for the identification of P. insidiosum. The potential use of the assay directly in clinical samples is also discussed.
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Affiliation(s)
- Navaporn Worasilchai
- Interdisciplinary Program, Medical Microbiology, Chulalongkorn University, Bangkok, Thailand
| | - Piyasak Chaumpluk
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, India
| | - Ariya Chindamporn
- Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Omrani-Nava V, Hedayatizadeh-Omran A, Alizadeh-Navaei R, Mokhberi V, Jalalian R, Janbabaei G, Amjadi O, Rahmatpour G, Mozaffari A. TP53 single nucleotide polymorphism (rs1042522) in Iranian patients with coronary artery disease. Biomed Rep 2018; 9:259-265. [PMID: 30271603 PMCID: PMC6158393 DOI: 10.3892/br.2018.1121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 06/22/2018] [Indexed: 02/05/2023] Open
Abstract
Chronic diseases including coronary artery disease (CAD) impose a high burden in terms of mortality and disability particularly in developing countries. Both genetic and environmental risk factors confer susceptibility to CAD. Meanwhile, a functional polymorphism in the tumor protein p53 (TP53) gene (codon 72, exon 4) has been reported to be associated with a wide range of cancers and inflammatory disorders. There are controversies regarding CAD and involvement of the TP53 codon 72 single nucleotide polymorphism; therefore, the present case-control study was conducted to evaluate the potential association between this TP53 polymorphism and CAD in an Iranian population. A total of 153 subjects (including 70 patients diagnosed with CAD and 83 subjects with normal coronary parameters, determined by angiography) were genotyped for the TP53 (rs1042522) polymorphism by the polymerase chain reaction-restriction fragment length polymorphism technique. Clinical and laboratory findings were also evaluated. The χ2 test and unpaired Student's t-test were applied to compare genotype and allele distributions and clinical characteristics between the two groups. Significant associations of the Pro72 allele [odds ratio (OR)=1.66, P=0.027] and Pro/Pro genotype (OR=2.91, P=0.022) with CAD were identified. No associations between patients' clinical findings and genotypes were apparent. Therefore, according to present findings, the TP53 Pro72 allele may be involved in the development of CAD along with conventional risk factors in patients from Northern Iran.
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Affiliation(s)
- Versa Omrani-Nava
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48166-33131, Iran
| | - Akbar Hedayatizadeh-Omran
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48166-33131, Iran
- Correspondence to: Dr Akbar Hedayatizadeh-Omran, Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, 70 Razi Street, Sari, Mazandaran 48166-33131, Iran, E-mail:
| | - Reza Alizadeh-Navaei
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48166-33131, Iran
| | - Vahid Mokhberi
- Cardiovascular Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48471-91971, Iran
| | - Rozita Jalalian
- Cardiovascular Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48471-91971, Iran
| | - Ghasem Janbabaei
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48166-33131, Iran
| | - Omolbanin Amjadi
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48166-33131, Iran
| | - Ghasem Rahmatpour
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48166-33131, Iran
| | - Amir Mozaffari
- Gastrointestinal Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Mazandaran 48166-33131, Iran
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Zivdari M, Hejazi SH, Mirhendi SH, Jafari R, Rastegar HA, Abtahi SM. Molecular Identification of Leishmania Parasites in Sand Flies (Diptera, Psychodidae) of an Endemic Foci in Poldokhtar, Iran. Adv Biomed Res 2018; 7:124. [PMID: 30211137 PMCID: PMC6124214 DOI: 10.4103/abr.abr_207_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background: Cutaneous leishmaniasis is one of the most important public health problems in many developing countries. Sand flies, as vectors, transmit infectious forms of the parasite to the vertebrate hosts. Poldokhtar, South West of Iran, is one of the endemic foci of diseases with a little information about it. In this paper, we have tried to gather some useful information to control and to prevent this disease in this region. Materials and Methods: The present study was conducted to determine the vector(s), the parasite, and the species composition of sand flies in the Poldokhtar County during the months from July to September 2015. Sticky paper traps were used to collect sand flies from July to September. Species identification was done based on available diagnostic keys. Nested-polymerase chain reaction was performed to diagnosis the Leishmania infection of sand flies, and restriction fragment length polymorphism was used to identify the Leishmania species. Results: A total of 2000 specimens comprising 8 species of sand flies (6 Phlebotomus and 2 Sergentomyia) were identified. Phlebotomus papatasi was the dominant species outdoor and Sergentomyia sintoni was the dominant species indoor. Among the 163 specimens of female P. papatasi, just 10 of them (6.1%) were positive to Leishmania major parasites. Conclusion: This is the first report of Leishmania infection of P. papatasi to L. major in this region. The results revealed that the high density of P. papatasi in outdoor and their infection with L. major is attributed that this species can play a major role as a principle vector in this region.
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Affiliation(s)
- Masoomeh Zivdari
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Hossein Hejazi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Hossein Mirhendi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Reza Jafari
- Isfahan Health Training and Research Center, Institute Public of Health Researches, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan-Ali Rastegar
- Department of Health Center, Poledokhtar Health Center, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Seyed Mohammad Abtahi
- Department of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Abstract
Background Graves' disease (GD) is a multifactorial autoimmune disease with contribution from both genetic and epigenetic factors in its causation. Association of genetic factors and GD has been extensively studied. Gene "protein tyrosine phosphatase nonreceptor 22" (PTPN22) is an important immunoregulatory gene preventing hyper responsiveness of T cells by negatively regulating their signal transduction. Association of single-nucleotide polymorphism (SNP) 1858 C/T within PTPN22 with some autoimmune diseases has been described. Methods We aimed to analyze whether 1858 C/T SNP of PTPN22 gene has any association with GD in Kashmiri population. Polymerase chain reaction-restriction fragment length polymorphism was performed for genotyping 1858 C/T SNP in 135 patients with GD and 150 age- and gender-matched healthy controls. Results Among the patients with GD, the frequencies of PTPN22 1858 CC, CT, and TT genotypes were 97.7, 2.2, and 0%, respectively, whereas in healthy controls the frequencies of CC, CT genotypes were 100 and 0%, respectively. No significant association was found between PTPN22 1858 C/T SNP and patients with GD. Conclusion GD is not associated with PTPN22 1858 C/T SNP in Kashmiri population. Furthermore, 1858 C/T SNP in PTPN22 gene could be a part of variation in different ethnic populations across the globe.
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Affiliation(s)
- Faheem Shehjar
- Department of Endocrinology, Sher-i-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, Jammu and Kashmir, India
| | - Dil-Afroze
- Department of Immunology and Molecular Medicine, Sher-i-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, Jammu and Kashmir, India
| | - Riaz A Misgar
- Department of Endocrinology, Sher-i-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, Jammu and Kashmir, India
| | - Sajad A Malik
- Department of Endocrinology, Sher-i-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, Jammu and Kashmir, India
| | - Bashir A Laway
- Department of Endocrinology, Sher-i-Kashmir Institute of Medical Sciences (SKIMS), Srinagar, Jammu and Kashmir, India
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You Y, Wang X, Li S, Zhao X, Zhang X. Exome sequencing reveals a novel MFN2 missense mutation in a Chinese family with Charcot-Marie-Tooth type 2A. Exp Ther Med 2018; 16:2281-2286. [PMID: 30210586 PMCID: PMC6122517 DOI: 10.3892/etm.2018.6513] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/08/2018] [Indexed: 12/20/2022] Open
Abstract
Charcot-Marie-Tooth (CMT) is a group of inherited peripheral neuropathies. To date, mutations in >80 genes are reportedly associated with CMT. Protein mitofusin 2 encoded by MFN2 serves an essential role in mitochondrial fusion and regulation of apoptosis, which has previously been reported to be highly associated with an axonal form of neuropathy (CMT2A). In the present study, a large Chinese family with severe CMT was reported and a genetic analysis of the disease was performed. A detailed physical examination for CMT was performed in 13 family members and electrophysiological examinations were performed in 3 affected family members. Whole-exome sequencing was performed on the proband, and the suspected variants were identified by Sanger sequencing. The pathogenicity of mutation was verified by restriction fragment length polymorphism analysis in the family followed by a bioinformatics analysis. A novel c.1190G>C; p.(R397P) mutation in the MFN2 gene was identified in the proband, and co-segregated between genotype and phenotype in the family. The substituted amino acid changed the hydrophobicity and charge characteristics of the mitofusin 2 coiled-coiled domain; thus it may affect its biological function. In summary, a novel pathogenic mutation was identified in a Chinese family with CMT, which expands the phenotypic and mutational spectrum of CMT2A, and provides evidence for prenatal interventions and more precise pharmacological treatments to this family.
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Affiliation(s)
- Yi You
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiaodong Wang
- Department of Paediatric Orthopaedics, The Children's Hospital of Soochow University, Suzhou, Jiangsu 215000, P.R. China
| | - Shan Li
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiuli Zhao
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P.R. China
| | - Xue Zhang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P.R. China
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García JC, LaFrentz BR, Waldbieser GC, Wong FS, Chang SF. Characterization of atypical Flavobacterium columnare and identification of a new genomovar. J Fish Dis 2018; 41:1159-1164. [PMID: 29697149 DOI: 10.1111/jfd.12778] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/17/2017] [Accepted: 12/05/2017] [Indexed: 06/08/2023]
Affiliation(s)
- J C García
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - B R LaFrentz
- Aquatic Animal Health Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Auburn, AL, USA
| | - G C Waldbieser
- USDA-ARS, Warmwater Aquaculture Research Unit, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, USA
| | - F S Wong
- MSD Animal Health, MSD Animal Health Innovation Pte Ltd, Singapore City, Singapore
| | - S F Chang
- MSD Animal Health, MSD Animal Health Innovation Pte Ltd, Singapore City, Singapore
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Ferroglio E, Battisti E, Zanet S, Bolla C, Concialdi E, Trisciuoglio A, Khalili S, Biglino A. Epidemiological evaluation of Leishmania infantum zoonotic transmission risk in the recently established endemic area of Northwestern Italy. Zoonoses Public Health 2018; 65:675-682. [PMID: 29745468 DOI: 10.1111/zph.12477] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Indexed: 11/26/2022]
Abstract
Leishmania infantum infection had been expanding into new areas due to changes in vector and host biology. Zoonotic visceral leishmaniasis has become endemic in previously unsuitable areas as vectors find favourable climatic conditions and an increasing number of reservoir dogs are moved between traditionally and new endemic areas. Monitoring vector and disease expansion in areas of recent colonization is needed to understand transmission mechanisms and patterns of disease establishment. Here, we studied the infection status of 815 human blood donors and of 803 sympatric dogs from five, newly endemic, areas in Northwestern Italy. In autochthonous dogs, the seroprevalence of anti-L. infantum antibodies, recorded by Western blot, reached 42.22%, while in humans, the seroprevalence was of 16.81%. No significant correlation between the infection status of dogs and that of their human owners was found, but L. infantum infection was recorded in the different study areas with significant levels of diversity. Restriction fragment length polymorphism showed a high genetic variability of the circulating strains and gave useful insights on patterns of disease establishment into a naïve area.
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Affiliation(s)
- E Ferroglio
- Department of Veterinary Sciences, University of Turin, Torino, Italy
| | - E Battisti
- Department of Veterinary Sciences, University of Turin, Torino, Italy
| | - S Zanet
- Department of Veterinary Sciences, University of Turin, Torino, Italy
| | - C Bolla
- Department of Clinical and Biological Sciences, Azienda Ospedaliero-Universitaria San Luigi Gonzaga, University of Turin, Torino, Italy
| | - E Concialdi
- Department of Clinical and Biological Sciences, Azienda Ospedaliero-Universitaria San Luigi Gonzaga, University of Turin, Torino, Italy
| | - A Trisciuoglio
- Department of Veterinary Sciences, University of Turin, Torino, Italy
| | - S Khalili
- Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - A Biglino
- Department of Clinical and Biological Sciences, Azienda Ospedaliero-Universitaria San Luigi Gonzaga, University of Turin, Torino, Italy
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Alavian SE, Sharafi H, Shirmast P, Alavian SM, Behnava B, Pouryasin M, Keshvari M, Pouryasin A. A facile PCR-RFLP method for genotyping of ITPA rs1127354 and rs7270101 polymorphisms. J Clin Lab Anal 2018; 32:e22440. [PMID: 29660762 DOI: 10.1002/jcla.22440] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 03/02/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Inosine triphosphate pyrophosphatase (ITPA) gene single nucleotide polymorphisms (SNPs), rs1127354 and rs7270101, may cause a functional impairment in ITPase enzyme, resulting anemia protection in patients with chronic hepatitis C virus (HCV) infection undergoing ribavirin (RBV)-dependent regimens. The main purpose of this study was to provide and validate a simple, rapid, and inexpensive polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique for genotyping of ITPA rs1127354 and rs7270101 polymorphisms in chronic HCV-infected patients. METHODS In the current study, 100 Iranian patients with chronic hepatitis C were examined and genotyped for ITPA rs1127354 and rs7270101 gene polymorphisms. To genotype rs1127354 and rs7270101 polymorphisms, PCR-RFLP technique and sequencing technique were performed on these samples. To validate the PCR-RFLP method, the PCR-RFLP genotyping results should be 100% concordant with the PCR-sequencing results. RESULTS The rs1127354 and rs7270101 polymorphisms of ITPA gene were genotyped by PCR-RFLP technique and sequencing simultaneously, and the results of both techniques were 100% concordant in all 100 patients. Both PCR-RFLP and sequencing techniques indicated that the genotypic frequency of rs7270101 was 80% AA, 19% AC and 1% CC, and for rs1127354 was 79% CC, 20% CA and 1% AA, respectively. CONCLUSION We developed and validated a rapid and inexpensive PCR-RFLP technique for the detection of ITPA rs1127354 and rs7270101 gene polymorphisms.
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Affiliation(s)
- Seyed Ehsan Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Middle East Liver Diseases (MELD) Virology Laboratory, MELD Center, Tehran, Iran
| | - Heidar Sharafi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Middle East Liver Diseases (MELD) Virology Laboratory, MELD Center, Tehran, Iran
| | - Paniz Shirmast
- Middle East Liver Diseases (MELD) Virology Laboratory, MELD Center, Tehran, Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Bita Behnava
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Maryam Keshvari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
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Javid F, Taku A, Bhat MA, Badroo GA, Mudasir M, Sofi TA. Molecular typing of Staphylococcus aureus based on coagulase gene. Vet World 2018; 11:423-430. [PMID: 29805205 PMCID: PMC5960779 DOI: 10.14202/vetworld.2018.423-430] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/27/2018] [Indexed: 12/02/2022] Open
Abstract
Aim This study was conducted to study the coagulase gene-based genetic diversity of Staphylococcus aureus, isolated from different samples of cattle using restriction fragment length polymorphism (RFLP) and their sequence-based phylogenetic analysis. Materials and Methods A total of 192 different samples from mastitic milk, nasal cavity, and pus from skin wounds of cattle from Military Dairy Farm, Jammu, India, were screened for the presence of S. aureus. The presumptive isolates were confirmed by nuc gene-based polymerase chain reaction (PCR). The confirmed S. aureus isolates were subjected to coagulase (coa) gene PCR. Different coa genotypes observed were subjected to RFLP using restriction enzymes Hae111 and Alu1, to obtain the different restriction patterns. One isolate from each restriction pattern was sequenced. These sequences were aligned for maximum homology using the Bioedit softwareandsimilarity in the sequences was inferred with the help of sequence identity matrix. Results Of 192 different samples,39 (20.31%) isolates of S. aureus were confirmed by targeting nuc gene using PCR. Of 39 S. aureus isolates, 25 (64.10%) isolates carried coa gene. Four different genotypes of coa gene, i.e., 514 bp, 595 bp, 757 bp, and 802 bp were obtained. Two coa genotypes, 595 bp (15 isolates) and 802 bp (4 isolates), were observed in mastitic milk. 514 bp (2 isolates) and 757 bp (4 isolates) coa genotypes were observed from nasal cavity and pus from skin wounds, respectively. On RFLP using both restriction enzymes, four different restriction patterns P1, P2, P3, and P4 were observed. On sequencing, four different sequences having unique restriction patterns were obtained. The most identical sequences with the value of 0.810 were found between isolate S. aureus 514 (nasal cavity) and S. aureus 595 (mastitic milk), and thus, they are most closely related. While as the most distant sequences with the value of 0.483 were found between S. aureus 514 and S. aureus 802 isolates. Conclusion The study, being localized to only one farm, yielded different RFLP patterns as observed from different sampling sites, which indicates that different S. aureus coagulase typeshave a site-specific predilection. Two coa patterns were observed in mastitic milk indicating multiple origins of infection, with 595 bp coa genotype being predominant in mastitic milk. The coa genotypes and their restriction patterns observed in the present study are novel, not published earlier. 514 and 595 coa variants of S. aureus are genetically most related.
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Affiliation(s)
- Faizan Javid
- Bacteriology Laboratory, Division of Veterinary Microbiology and Immunology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu and Kashmir, India
| | - Anil Taku
- Bacteriology Laboratory, Division of Veterinary Microbiology and Immunology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu and Kashmir, India
| | - Mohd Altaf Bhat
- Bacteriology Laboratory, Division of Veterinary Microbiology and Immunology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu and Kashmir, India
| | - Gulzar Ahmad Badroo
- Bacteriology Laboratory, Division of Veterinary Microbiology and Immunology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu and Kashmir, India
| | - Mir Mudasir
- Division of Veterinary Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu and Kashmir, India
| | - Tanveer Ahmad Sofi
- Division of Animal Genetics and Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu and Kashmir, India
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Pašalić D, Marinković N. Genetic polymorphisms of the CYP1A1, GSTM1, and GSTT1 enzymes and their influence on cardiovascular risk and lipid profile in people who live near a natural gas plant. Arh Hig Rada Toksikol 2017; 68:46-52. [PMID: 28365671 DOI: 10.1515/aiht-2017-68-2772] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 03/01/2017] [Indexed: 11/15/2022] Open
Abstract
The aim of this cross-sectional study was to see whether genetic polymorphisms of the enzymes CYP1A1, GSTM1, and GSTT1 are associated with higher risk of coronary artery disease (CAD) and whether they affect lipid profile in 252 subjects living near a natural gas plant, who are likely to be exposed to polycyclic aromatic hydrocarbons (PAHs). Fasting serum concentrations of biochemical parameters were determined with standard methods. Genetic polymorphisms of CYP 1A1 rs4646903, rs1048943, rs4986883, and rs1799814 were genotyped with polymerase chain reaction-restriction fragment length polymorphism (PCR-RFPL), while GSTM1 and GSTT1 deletions were detected with multiplex PCR. Cardiovascular risk was assessed with Framingham risk score, and the subjects divided in two groups: >10% risk and ≤10% risk. The two groups did not differ in the genotype frequencies. MANCOVA analysis, which included lipid parameters, glucose, and BMI with sex, age, hypertension and smoking status as covariates, showed a significant difference between the GSTT1*0 and GSTT1*1 allele carriers (p=0.001). UNIANCOVA with same covariates showed that total cholesterol and triglyceride levels were significantly higher in GSTT1*1 allele carriers than in GSTT1*0 carriers (p<0.001 and p=0.006, respectively). Our findings suggest that CYP1A1, GSTM1, and GSTT1 polymorphisms are not associated with the higher risk of CAD, but that GSTT1 affects lipid profile.
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Affiliation(s)
- Daria Pašalić
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, Zagreb University School of Medicine, Zagreb
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Karimi S, Mirhendi H, Zaniani FR, Manesh SE, Salehi M, Esfahani BN. Rapid Detection of Streptomycin-Resistant Mycobacterium tuberculosis by rpsL- Restriction Fragment Length Polymorphism. Adv Biomed Res 2017; 6:126. [PMID: 29142889 PMCID: PMC5672647 DOI: 10.4103/abr.abr_240_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background: Molecular methods for the detection of drug-resistant tuberculosis (DR-TB) are potentially more rapid than conventional culture-based drug susceptibility testing, facilitating the commencement of appropriate treatment for patients with DR-TB. The aim of this study was to evaluate and develop polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assays for the detection of mutations within rpsL, and for the determination of streptomycin (STR) resistance in Mycobacterium tuberculosis. Materials and Methods: Clinical specimens were collected from individuals with suspected TB referred to the TB Center of Isfahan, from which 205 M. tuberclosis were isolated and identified by conventional phenotypic methods. The minimum inhibitory concentration of STR for all isolates was determined using the proportion method and 10 isolates were recognized as STR resistant M. tuberculosis. The effect of genetic alterations in the rpsL gene for these resistant isolates were investigated by PCR-RFLP method. Results: Three (30%) isolates showed point mutation at codon 43 by RLFP analysis. Conclusion: Our results suggest that RFLP analysis of the rpsL gene is useful for the rapid prediction of STR resistant strains of M. tuberculosis.
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Affiliation(s)
- Sediqe Karimi
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemh Riyahi Zaniani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Soroor Erfani Manesh
- Department of Microbiology, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahshd Salehi
- Mollahadi Sabzevari Tuberculosis Center, Isfahan, Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Diab SM, Kamal HM, Mansour AI, Fawzy RM, Azab BS. Clinical significance of Matrilin-3 gene polymorphism in Egyptian patients with primary knee osteoarthritis. Eur J Rheumatol 2017; 4:200-204. [PMID: 28983412 PMCID: PMC5621842 DOI: 10.5152/eurjrheum.2016.16107] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 03/05/2017] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE Osteoarthritis (OA) is a multifactorial, degenerative, and inflammatory disorder of joints causing damage of the articular cartilage, formation of osteophytes, and eburination of the subchondral bone. Matrilin-3 (MATN-3) is a non-collagenous oligomeric extracellular matrix protein (ECM), which is the smallest member of the matrilin family. This study was conducted to identify the potential association and clinical significance of MATN-3 rs8176070 (SNP6) polymorphism in a series of Egyptian patients with primary knee OA. MATERIAL AND METHODS Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to determine genotypes of MATN-3 SNP6 for 50 primary knee OA patients in addition to 50 healthy subjects of the same sex and age range. Full history was obtained from OA patients, followed by clinical examination, together with clinical assessment of the severity of knee OA using Lequesne Algofunctional Index score and radiological grading using the Kellgren-Lawrence grade scale (KL). RESULTS With regard to genotypes of MATN-3 gene SNP6 (rs8176070), a statistically significant difference between OA patients and healthy control subjects was found for the B\b genotype and b allele (p=0.046 and 0.042 respectively), with the prevalence being higher in OA patients with a high risk to develop OA (Odds Ratio [OR]=2.250, 95% CI=1.011-5.008). Patients with the B\b genotype had worse clinical and radiological findings than those with B\B and b\b genotypes. CONCLUSION The investigated polymorphism in the MATN-3 gene may reflect the risk and severity of knee OA in Egyptian patients, particularly with the B\b genotype.
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Affiliation(s)
- Safia M. Diab
- Department of Clinical & Chemical Pathology, Benha University School Medicine, Benha, Egypt
| | - Howyda M. Kamal
- Department of Clinical & Chemical Pathology, Benha University School Medicine, Benha, Egypt
| | - Amira I. Mansour
- Department of Clinical & Chemical Pathology, Benha University School Medicine, Benha, Egypt
| | - Rasha M. Fawzy
- Department of Rheumatology & Rehabilitation, Benha University School Medicine, Benha, Egypt
| | - Basma S. Azab
- Department of Clinical & Chemical Pathology, Benha University School Medicine, Benha, Egypt
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LaFrentz BR, García JC, Dong HT, Waldbieser GC, Rodkhum C, Wong FS, Chang SF. Optimized reverse primer for 16S-RFLP analysis and genomovar assignment of Flavobacterium columnare. J Fish Dis 2017; 40:1103-1108. [PMID: 27982441 DOI: 10.1111/jfd.12583] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/18/2016] [Accepted: 10/18/2016] [Indexed: 06/06/2023]
Affiliation(s)
- B R LaFrentz
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aquatic Animal Health Research Unit, Auburn, AL, USA
| | - J C García
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aquatic Animal Health Research Unit, Auburn, AL, USA
| | - H T Dong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Department Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - G C Waldbieser
- USDA-ARS, Warmwater Aquaculture Research Unit, Thad Cochran National Warmwater Aquaculture Center, Stoneville, MS, USA
| | - C Rodkhum
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - F S Wong
- MSD Animal Health, MSD Animal Health Innovation Pte Ltd, Singapore city, Singapore
| | - S F Chang
- MSD Animal Health, MSD Animal Health Innovation Pte Ltd, Singapore city, Singapore
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Khubaib B, Idrees M, Fatima Z, Akram M, Afzal S, Amin I, Shahid M, Wasim M. Evaluation of three techniques for detection of IL28B SNP: A prognostic tool for HCV treatment outcome. J Dig Dis 2017; 18:404-409. [PMID: 28608576 DOI: 10.1111/1751-2980.12497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 05/16/2017] [Accepted: 06/08/2017] [Indexed: 12/11/2022]
Abstract
OBJECTIVE The study was aimed to evaluate the specificity, cost and turnaround time of three different techniques that can be used for analyzing the single nucleotide polymorphism of interleukin 28B (IL28B) rs129796860. METHODS DNA from peripheral blood samples of 111 patients with chronic hepatitis C were genotyped using three types of genotyping methods: direct sequencing, SNaPshot polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP). RESULTS Three distinct profiles for IL28B rs12979860 alleles (CC, CT and TT) were obtained with direct sequencing, SNaPshot PCR and PCR-RFLP and the results were consistent among all three methods. CONCLUSION For routine medical practice, screening IL28B rs12979860 can be performed by PCR-RFLP, which is efficient and reliable as well as cost-effective.
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Affiliation(s)
- Bushra Khubaib
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Idrees
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Zareen Fatima
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Madiha Akram
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Samia Afzal
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Iram Amin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Shahid
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Wasim
- Genome Center for Molecular-based Diagnostics & Research, CL-25, Abdalian Cooperative Housing Society Lahore, Lahore, Pakistan
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Monavari SH, Fateh R, Vaziri F, Rahimi Jamnani F, Anvari E, Sadeghi F, Afrough P, Behrouzi A, Sakhaee F, Meidaninikjeh S, Mollaie H, Hadizadeh Tasbiti A, Yari S, Sadeghi M, Fateh A, Siadat SD. A comparative study of various methods for detection of IL28B rs12979860 in chronic hepatitis C. Scand J Clin Lab Invest 2017; 77:247-252. [PMID: 28281380 DOI: 10.1080/00365513.2017.1299207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Interleukin-28B (IL28B) single-nucleotide polymorphisms (SNPs) constitute important host-related factors influencing the response rate to Hepatitis C virus (HCV) standard antiviral therapy. In the last few years, several new technologies for SNP detection have been developed. However, the sensitivity and specificity of various methods are different and needs evaluation. Five different methods (resolution melting curve [RMC], polymerase chain reaction-restriction fragment length polymorphism [PCR-RFLP], PCR-sequencing analysis, amplification refractory mutation system [ARMS], and zip nucleic acid probe-based real-time PCR [ZNA]) were developed for genotyping rs12979860 associated with IL28B. In this study, limit of detection (LD), costs and turnaround time of these methods were compared in 350 subjects. As for IL28B rs12979860 polymorphisms, 348/350 (99.4%) samples were consistent among the five methods, while results for 2/350 (0.57%) samples were concordant by ZNAs and PCR-sequencing, and discordant by other methods. Without considering the cost of DNA extraction, the price of each reaction for ARMS-PCR, RMC, PCR-RFLP, ZNA and PCR-sequencing were respectively: US$3.10, US$5.0, US$5.50, US$8.50 and US$17.0. RMC was the fastest method, while the ZNA method was easy to use, reliable and effective. Lower LD was determined to be 50-60 copies/μL for the PCR-RFLP, RMC and ARMS-PCR assays; whilst ZNA assay was able to detect 2-3 copies/μL. In conclusion, in the current study, all four methods are suitable for IL28B rs12979860 genotyping, but the ZNA assay can be a reliable tool. Due to its lower LD for SNP identification, this method is better than others for detecting this type of polymorphism.
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Affiliation(s)
| | - Roohollah Fateh
- b Department of Microbiology and Immunology, Faculty of Medicine , Qom University of Medical Sciences , Qom , Iran
| | - Farzam Vaziri
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
- d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran
| | - Fatemeh Rahimi Jamnani
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
- d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran
| | - Enayat Anvari
- e Department of Physiology, Faculty of Medicine , Ilam University of Medical Sciences , Ilam , Iran
| | - Farzin Sadeghi
- f Department of Immunology and Microbiology , Babol University of Medical Sciences, School of Medicine , Babol , Iran
| | - Parviz Afrough
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
- d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran
| | - Ava Behrouzi
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
| | - Fatemeh Sakhaee
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
| | - Sepideh Meidaninikjeh
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
| | - Hamidreza Mollaie
- g Department of Medical Virology , Kerman University of Medical Sciences , Kerman , Iran
| | | | - Shamsi Yari
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
| | - Maryam Sadeghi
- h Department of English , Mahshahr Branch, Islamic Azad University , Mahshahr , Iran
| | - Abolfazl Fateh
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
- d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran
| | - Seyed Davar Siadat
- c Department of Mycobacteriology and Pulmonary Research , Pasteur Institute of Iran , Tehran , Iran
- d Microbiology Research Center (MRC) , Pasteur Institute of Iran , Tehran , Iran
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Frikha R, Bouayed N, Ben Rhouma B, Keskes L, Rebai T. A duplex polymerase chain reaction- restriction fragment length polymorphism for rapid screening of methylenetetrahydrofolate reductase gene variants: Genotyping in acute leukemia. J Clin Lab Anal 2017; 32. [PMID: 28374953 DOI: 10.1002/jcla.22198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 02/17/2017] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Methylenetetrahydrofolate reductase (MTHFR; NM_005957.4) is the key enzyme for folate metabolism which plays in DNA biosynthesis and the epigenetic process of DNA methylation. MTHFR gene polymorphisms, the c. 677C>T and c. 1298A>C have been implicated as risk factors for several types of cancers as the acute leukemia. AIM We have optimized a duplex polymerase chain reaction-restriction fragment length polymorphism assay (PCR-RFLP) for the simultaneous detection of both variants in acute leukemia patients, from Tunisia. METHODS Genomic DNA was extracted from EDTA-anticoagulant blood samples from a total of 50 patients suffering from acute leukemia (AL). After DNA extraction, the polymerase chain reaction using specific primers, designed using Primer 3 Software. Restriction Fragment Length Polymorphism (RFLP) was performed in two separate tubes followed by agarose gel electrophoresis. CONCLUSION This new method has proved to be a rapid, simple, and reliable method that should facilitate high throughput genotyping of MTHFR polymorphisms in acute leukemia.
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Affiliation(s)
- Rim Frikha
- Laboratory of Histology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Nouha Bouayed
- Laboratory of Histology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Bochra Ben Rhouma
- Laboratory of Histology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Leila Keskes
- Laboratory of Histology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Tarek Rebai
- Laboratory of Histology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
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Jain V, Patel B, Umar FP, Ajithakumar HM, Gurjar SK, Gupta ID, Verma A. Identification of single nucleotide polymorphism in protein phosphatase 1 regulatory subunit 11 gene in Murrah bulls. Vet World 2017; 10:244-248. [PMID: 28344410 PMCID: PMC5352852 DOI: 10.14202/vetworld.2017.244-248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 01/23/2017] [Indexed: 11/19/2022] Open
Abstract
Aim: This study was conducted with the objective to identify single nucleotide polymorphism (SNP) in protein phosphatase 1 regulatory subunit 11 (PPP1R11) gene in Murrah bulls. Materials and Methods: Genomic DNA was isolated by phenol–chloroform extraction method from the frozen semen samples of 65 Murrah bulls maintained at Artificial Breeding Research Centre, ICAR-National Dairy Research Institute, Karnal. The quality and concentration of DNA was checked by spectrophotometer reading and agarose gel electrophoresis. The target region of PPP1R11 gene was amplified using four sets of primer designed based on Bos taurus reference sequence. The amplified products were sequenced and aligned using Clustal Omega for identification of SNPs. Animals were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) using EcoNI restriction enzyme. Results: The sequences in the NCBI accession number NW_005785016.1 for Bubalus bubalis were compared and aligned with the edited sequences of Murrah bulls with Clustal Omega software. A total of 10 SNPs were found, out of which 1 at 5’UTR, 3 at intron 1, and 6 at intron 2 region. PCR-RFLP using restriction enzyme EcoNI revealed only AA genotype indicating monomorphism in PPP1R11 gene of all Murrah animals included in the study. Conclusion: A total of 10 SNPs were found. PCR-RFLP revealed only AA genotype indicating monomorphism in PPP1R11 gene of all Murrah animals included in the study, due to which association analysis with conception rate was not feasible.
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Affiliation(s)
- Varsha Jain
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Brijesh Patel
- Livestock Production Management Section, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Farhat Paul Umar
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - H M Ajithakumar
- Division of Animal Physiology, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Suraj K Gurjar
- Division of Animal Physiology, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - I D Gupta
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Archana Verma
- Division of Animal Genetics and Breeding, ICAR-National Dairy Research Institute, Karnal, Haryana, India
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Tichy ED, Mourkioti F. A new method of genotyping MDX 4CV mice by PCR-RFLP analysis. Muscle Nerve 2017; 56:522-524. [PMID: 28063157 DOI: 10.1002/mus.25566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 12/31/2022]
Abstract
INTRODUCTION The mdx4cv mouse is a common model to study Duchenne muscular dystrophy. The most used methodology to identify the genotype of these mice is Sanger DNA sequencing. METHODS Here, we provide a simple, cost-effective alternative approach to identify the wild-type, heterozygous, or homozygous/hemizygous genotypes of these mice, using commonly available laboratory equipment and reagents. RESULTS Our technique exploits a restriction fragment length polymorphism that is generated by the point mutation found in exon 53 of mdx4cv mice. CONCLUSIONS This technique can benefit laboratories that require complex breeding strategies involving mdx4cv mice. Muscle Nerve 56: 522-524, 2017.
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Affiliation(s)
- Elisia D Tichy
- Department of Orthopaedic Surgery, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Foteini Mourkioti
- Department of Orthopaedic Surgery, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Cell and Developmental Biology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
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Pouryasin M, Sharafi H, Behnava B, Alavian SM, Keshvari M, Pouryasin A. A Simple PCR-RFLP Method for Genotyping of IFNL4 rs368234815 Polymorphism in Patients With Chronic Hepatitis C. Lab Med 2017; 48:51-56. [PMID: 28057801 DOI: 10.1093/labmed/lmw060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The IFNL4 rs368234815 polymorphism plays a prominent role in spontaneous and treatment-induced clearance of hepatitis C virus (HCV) infection. This study aimed to develop a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method for assessment of rs368234815 polymorphism. METHODS We genotyped the rs368234815 polymorphism in 87 patients with chronic HCV by PCR sequencing and PCR-RFLP methods, simultaneously. RESULTS Genotyping of IFNL4 rs368234815 via PCR-RFLP was concordant with PCR sequencing in all 87 individuals (100%). The analytical sensitivity and specificity of the developed PCR-RFLP method for genotyping of rs368234815 polymorphism were each 100%. Among these patients with chronic HCV, the frequency of rs368234815 TT/TT, TT/ΔG, and ΔG/ΔG were 44.8%, 37.9%, and 17.3%, respectively. CONCLUSIONS The PCR-RFLP method that we developed is accurate, rapid, inexpensive, and easy to perform for genotyping of the IFNL4 rs368234815 polymorphism. This method can be used for clinical and research work.
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Affiliation(s)
- Mohammad Pouryasin
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Armin Pathobiology Laboratory, Tehran, Iran
| | - Heidar Sharafi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Armin Pathobiology Laboratory, Tehran, Iran.,Middle East Liver Diseases (MELD) Center, Tehran, Iran
| | - Bita Behnava
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Middle East Liver Diseases (MELD) Center, Tehran, Iran
| | - Seyed Moayed Alavian
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Middle East Liver Diseases (MELD) Center, Tehran, Iran
| | - Maryam Keshvari
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Ali Pouryasin
- Armin Pathobiology Laboratory, Tehran, Iran, .,Department of Biology, Arsanjan Branch, Islamic Azad University, Arsanjan, Iran
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Aristizábal-Pachón AF, Takahashi CS. [Effect of genetics, epigenetics and variations in the transcriptional expression of cadherin-E in breast cancer susceptibility]. Biomedica 2016; 36:593-602. [PMID: 27992986 DOI: 10.7705/biomedica.v36i4.3135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 04/25/2016] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Cadherin-E (CDH1) is an important regulator of epithelial-mesenchymal transition, invasion and metastasis in many carcinomas. However, germinal epimutations and mutations effect in breast cancer susceptibility is not clear. OBJECTIVE To evaluate rs334558 polymorphism, promoter methylation status and CDH1 expression profile in breast cancer patients. MATERIALS AND METHODS We collected peripheral blood samples from 102 breast cancer patients and 102 healthy subjects. The identification of rs334558 polymorphism was performed using PCR-RFLP, while methylation-specific PCR (MSP) and methylation-sensitive high-resolution melting (MS-HRM) were used to explore CDH1 methylation status; finally, CDH1 transcriptional expression profile was evaluated using RT-qPCR. RESULTS We found no association between rs334558 polymorphism and breast cancer. Aberrant promoter methylation profile was found in breast cancer patients and it was related with early cancer stages. CDH1 down-regulation was significantly associated with metastasis and promoter methylation. CONCLUSION CDH1 alterations were associated with invasion and metastasis in breast cancer. Our results offer further evidence of CDH1 relevance in breast cancer development and progression.
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Wang H, Sun H, Blackall PJ, Zhang Z, Zhou H, Xu F, Chen X. Evaluation of a proposed molecular methodology for the serotyping of Avibacterium paragallinarum. J Vet Diagn Invest 2016; 28:555-60. [PMID: 27423732 DOI: 10.1177/1040638716659523] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A multiplex (m)PCR and a PCR followed by restriction fragment length polymorphism (RFLP) analysis of Avibacterium paragallinarum have been proposed as alternatives to conventional serotyping by the Page scheme. We evaluated both methods, and also sequenced the PCR-RFLP target fragment to reexamine the capacity of molecular serotyping. Eleven reference strains and 27 field isolates were used. Many reference strains and isolates were misidentified as Page serogroup B. The sequence analysis revealed 6 profiles based on the matching rates of the target sequence with the 3 reverse primers of the mPCR. The reference strains and field isolates in profiles 1 and 4 were correctly identified as serogroup A or C by the mPCR. The strains and/or isolates in profiles 2, 3, 5, and 6 could be misidentified as serogroup B or as nontypeable by the mPCR. The homology comparison of the sequences showed that the target sequence of the mPCR, called region 2, was not Page serogroup specific, although some Kume serovars, such as A-1 and C-2, were correctly serotyped. In addition, there was a 9 nucleotide deletion in the sequences of profiles 1, 3, and 5, but not of profiles 2, 4, and 6. Overall, we confirmed that the mPCR and PCR-RFLP molecular assays are not suitable for identifying the serogroups of A. paragallinarum isolates. With further study, analysis of region 2 sequences may have potential as a means of recognizing the Kume serovars of A. paragallinarum isolates.
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Affiliation(s)
- Hongjun Wang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Municipal Academy of Agriculture and Forestry, Beijing, China (Wang, Sun, Zhang, Zhou, Xu, Chen)Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia (Blackall)
| | - Huiling Sun
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Municipal Academy of Agriculture and Forestry, Beijing, China (Wang, Sun, Zhang, Zhou, Xu, Chen)Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia (Blackall)
| | - Patrick J Blackall
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Municipal Academy of Agriculture and Forestry, Beijing, China (Wang, Sun, Zhang, Zhou, Xu, Chen)Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia (Blackall)
| | - Zhenhua Zhang
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Municipal Academy of Agriculture and Forestry, Beijing, China (Wang, Sun, Zhang, Zhou, Xu, Chen)Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia (Blackall)
| | - Hongzhuan Zhou
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Municipal Academy of Agriculture and Forestry, Beijing, China (Wang, Sun, Zhang, Zhou, Xu, Chen)Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia (Blackall)
| | - Fuzhou Xu
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Municipal Academy of Agriculture and Forestry, Beijing, China (Wang, Sun, Zhang, Zhou, Xu, Chen)Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia (Blackall)
| | - Xiaoling Chen
- Beijing Key Laboratory for Prevention and Control of Infectious Diseases in Livestock and Poultry, Institute of Animal Husbandry and Veterinary Medicine, Beijing Municipal Academy of Agriculture and Forestry, Beijing, China (Wang, Sun, Zhang, Zhou, Xu, Chen)Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia (Blackall)
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Huang K, Shen Y, Zhang F, Wang S, Wei X. Evaluation of effects of thymidylate synthase and excision repair cross-complementing 1 polymorphisms on chemotherapy outcome in patients with gastrointestinal tumors using peripheral venous blood. Oncol Lett 2016; 11:3477-3482. [PMID: 27123139 DOI: 10.3892/ol.2016.4423] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/01/2016] [Indexed: 11/06/2022] Open
Abstract
The aim of the present study was to evaluate the effects of thymidylate synthase (TYMS) and excision repair cross-complementing 1 (ERCC1) polymorphisms on chemotherapeutic efficacy in patients with gastrointestinal tumors using peripheral venous blood. Preoperative peripheral venous blood and tumor tissue samples of 43 patients with gastric cancer and the peripheral venous blood samples of 76 patients with cancer who underwent chemotherapy were studied. The 3R/3R and 2R/2R or 2R/3R genotypes of TYMS were identified in 72.09 and 27.91%, respectively (P<0.01), of untreated patients, and the C/C and T/T or C/T genotypes of ERCC1 were present in 81.39 and 18.61%, respectively (P<0.01), of patients. The 3R/3R and 2R/2R or 2R/3R genotypes of TYMS were identified in 65.79 and 34.21%, respectively, of chemotherapy-treated patients. The overall response rates (ORRs) for the two aforementioned genotypes were 18.00 and 57.69%, respectively (P<0.01), and those for the C/C and T/T or C/T genotypes of ERCC1 were 63.16 and 36.84%, respectively. The ORRs were 47.91 and 3.57%, respectively (P<0.01). In conclusion, peripheral blood samples may be used to replace tumor tissue for detecting TYMS and ERCC1 polymorphisms, and may be used to evaluate the efficacy of 5-fluorouracil and platinum drugs.
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Affiliation(s)
- Kaida Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yan Shen
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Fengqi Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Shanshan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Xiao Wei
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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Miyaguchi H, Yamamuro T, Ohta H, Nakahara H, Suzuki S. Genotyping of Toxic Pufferfish Based on Specific PCR-RFLP Products As Determined by Liquid Chromatography/Quadrupole-Orbitrap Hybrid Mass Spectrometry. J Agric Food Chem 2015; 63:9363-9371. [PMID: 26429637 DOI: 10.1021/acs.jafc.5b03703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A method based on liquid chromatography-electrospray mass spectrometric analysis of the enzymatically digested amplicons derived from the mitochondrial 16S rRNA gene was established for the discrimination of toxic pufferfish. A MonoBis C18 narrow-bore silica monolith column (Kyoto Monotech) and a Q Exactive mass spectrometer (Thermo Fisher) were employed for separation and detection, respectively. Monoisotopic masses of the oligonucleotides were calculated using Protein Deconvolution 3.0 software (Thermo Fisher). Although a lock mass standard was not used, excellent accuracy (mass error, 0.83 ppm on average) and precision (relative standard deviation, 0.49 ppm on average) were achieved, and a mass accuracy of <2.8 ppm was maintained for at least 180 h without additional calibration. The present method was applied to 29 pufferfish samples, and results were consistent with Sanger sequencing.
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Affiliation(s)
- Hajime Miyaguchi
- National Research Institute of Police Science , 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Tadashi Yamamuro
- National Research Institute of Police Science , 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Hikoto Ohta
- National Research Institute of Police Science , 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Hiroaki Nakahara
- National Research Institute of Police Science , 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Shinichi Suzuki
- National Research Institute of Police Science , 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
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